quarkus update

less commitSnapshots created
less bad read cache
2025-10-28 20:47:49 +01:00 · 2025-10-12 10:54:00 +02:00 · 2025-08-22 23:19:39 +02:00 · 2025-08-22 18:47:43 +02:00 · 2025-07-19 14:26:27 +02:00 · 2025-06-25 18:50:19 +02:00
197 changed files with 2691 additions and 1494 deletions
--- a/.dockerignore
+++ b/.dockerignore
@@ -1,4 +0,0 @@
-**/.parcel-cache
-**/dist
-**/node_modules
-**/target
--- a/.github/workflows/server.yml
+++ b/.github/workflows/server.yml
@@ -7,12 +7,6 @@ on:
  pull_request:
    branches: ["main"]

-env:
-  # Use docker.io for Docker Hub if empty
-  REGISTRY: ghcr.io
-  # github.repository as <account>/<repo>
-  IMAGE_NAME: ${{ github.repository }}
-
 jobs:
  build-dhfs:
    runs-on: ubuntu-latest
@@ -49,9 +43,6 @@ jobs:
      - name: Test with Maven
        run: cd dhfs-parent && mvn -T $(nproc) --batch-mode --update-snapshots package verify javadoc:aggregate

-      # - name: Build with Maven
-      #   run: cd dhfs-parent && mvn --batch-mode --update-snapshots package # -Dquarkus.log.category.\"com.usatiuk.dhfs\".min-level=DEBUG
-
      - uses: actions/upload-artifact@v4
        with:
          name: DHFS Server Package
@@ -92,107 +83,10 @@ jobs:
          name: Webui
          path: webui/dist

-  publish-docker:
-    runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      packages: write
-      # This is used to complete the identity challenge
-      # with sigstore/fulcio when running outside of PRs.
-      id-token: write
-
-    needs: [build-webui, build-dhfs]
-
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-
-      - name: Download server package
-        uses: actions/download-artifact@v4
-        with:
-          name: DHFS Server Package
-          path: dhfs-package-downloaded
-
-      - name: Download webui
-        uses: actions/download-artifact@v4
-        with:
-          name: Webui
-          path: webui-dist-downloaded
-
-      - name: Show all the files
-        run: find .
-
-      # Install the cosign tool except on PR
-      # https://github.com/sigstore/cosign-installer
-      - name: Install cosign
-        if: github.event_name != 'pull_request'
-        uses: sigstore/cosign-installer@v3.5.0
-        with:
-          cosign-release: "v2.2.4"
-
-      # Set up BuildKit Docker container builder to be able to build
-      # multi-platform images and export cache
-      # https://github.com/docker/setup-buildx-action
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
-      - name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
-      # Login against a Docker registry except on PR
-      # https://github.com/docker/login-action
-      - name: Log into registry ${{ env.REGISTRY }}
-        if: github.event_name != 'pull_request'
-        uses: docker/login-action@v3
-        with:
-          registry: ${{ env.REGISTRY }}
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-
-      # Extract metadata (tags, labels) for Docker
-      # https://github.com/docker/metadata-action
-      - name: Extract Docker metadata
-        id: meta
-        uses: docker/metadata-action@v5
-        with:
-          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
-
-      # Build and push Docker image with Buildx (don't push on PR)
-      # https://github.com/docker/build-push-action
-      - name: Build and push Docker image
-        id: build-and-push
-        uses: docker/build-push-action@v5
-        with:
-          context: .
-          file: ./Dockerfile.ci
-          push: ${{ github.event_name != 'pull_request' }}
-          platforms: linux/amd64,linux/arm64
-          tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
-          cache-from: type=gha
-          cache-to: type=gha,mode=max
-
-      # Sign the resulting Docker image digest except on PRs.
-      # This will only write to the public Rekor transparency log when the Docker
-      # repository is public to avoid leaking data.  If you would like to publish
-      # transparency data even for private images, pass --force to cosign below.
-      # https://github.com/sigstore/cosign
-      - name: Sign the published Docker image
-        if: ${{ github.event_name != 'pull_request' }}
-        env:
-          # https://docs.github.com/en/actions/security-guides/security-hardening-for-github-actions#using-an-intermediate-environment-variable
-          TAGS: ${{ steps.meta.outputs.tags }}
-          DIGEST: ${{ steps.build-and-push.outputs.digest }}
-        # This step uses the identity token to provision an ephemeral certificate
-        # against the sigstore community Fulcio instance.
-        run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST}
-
  publish-run-wrapper:
    runs-on: ubuntu-latest
    permissions:
      contents: read
-      packages: write
-      # This is used to complete the identity challenge
-      # with sigstore/fulcio when running outside of PRs.
-      id-token: write

    needs: [build-webui, build-dhfs]

@@ -225,6 +119,10 @@ jobs:
      - name: Copy run wrapper
        run: cp -r ./run-wrapper/* "run-wrapper-out/dhfs/app/"

+      - name: Copy README
+        run: |
+          cp README.md "run-wrapper-out/dhfs/"
+
      - name: Add version to run wrapper
        run: echo $GITHUB_RUN_ID > "run-wrapper-out/dhfs/app/"version

@@ -236,3 +134,36 @@ jobs:
        with:
          name: Run wrapper
          path: ~/run-wrapper.tar.gz
+
+  publish-javadoc:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pages: write
+      id-token: write
+
+    needs: [build-webui, build-dhfs]
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - uses: actions/download-artifact@v4
+        with:
+          name: DHFS Javadocs
+          path: dhfs-javadocs-downloaded
+
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: "dhfs-javadocs-downloaded"
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
--- a/.vscode/ltex.dictionary.en-US.txt
+++ b/.vscode/ltex.dictionary.en-US.txt
@@ -0,0 +1 @@
+Syncthing
--- a/35
+++ b/35
@@ -1,35 +0,0 @@
-FROM node:20-bullseye as webui-build
-
-WORKDIR /usr/src/app/webui-build
-COPY ./webui/package*.json ./
-RUN npm i
-COPY ./webui/. .
-RUN npm run build
-
-FROM azul/zulu-openjdk:21 as server-build
-
-WORKDIR /usr/src/app/server-build
-COPY ./server/.mvn .mvn
-COPY ./server/mvnw ./server/pom.xml ./
-RUN ./mvnw quarkus:go-offline
-# The previous thing still doesn't download 100% everything
-RUN ./mvnw -Dmaven.test.skip=true -Dskip.unit=true package --fail-never
-COPY ./server/. .   
-RUN ./mvnw -Dmaven.test.skip=true -Dskip.unit=true clean package
-
-FROM azul/zulu-openjdk-alpine:21-jre-headless
-
-RUN apk update && apk add fuse && rm -rf /var/cache/apk/*
-
-WORKDIR /usr/src/app
-COPY --from=server-build /usr/src/app/server-build/target/quarkus-app/. .
-RUN mkdir -p webui
-COPY --from=webui-build /usr/src/app/webui-build/dist/. ./webui
-
-ENV dhfs_webui_root=/usr/src/app/webui
-
-COPY ./dockerentry.sh .
-
-RUN ["chmod", "+x", "./dockerentry.sh"]
-
-CMD [ "./dockerentry.sh" ]
--- a/Dockerfile.ci
+++ b/Dockerfile.ci
@@ -1,22 +0,0 @@
-FROM azul/zulu-openjdk:21-jre-headless
-
-RUN apt update && apt install -y libfuse2 && apt-get clean
-
-WORKDIR /usr/src/app
-
-COPY ./dhfs-package-downloaded/lib .
-COPY ./dhfs-package-downloaded/*.jar .
-COPY ./dhfs-package-downloaded/app .
-COPY ./dhfs-package-downloaded/quarkus .
-
-WORKDIR /usr/src/app/webui
-COPY ./webui-dist-downloaded/. .
-
-ENV dhfs_webui_root=/usr/src/app/webui
-
-WORKDIR /usr/src/app
-COPY ./dockerentry.sh .
-
-RUN ["chmod", "+x", "./dockerentry.sh"]
-
-CMD [ "./dockerentry.sh" ]
--- a/README.md
+++ b/README.md
@@ -1,4 +1,6 @@
-# Distributed Home File System 🚧
+# Distributed Home File System
+
+[Javadocs](https://usatiuk.github.io/dhfs/)

 ## What is this?

@@ -11,12 +13,78 @@ Syncthing and allowing you to stream your files like Google Drive File Stream

 [Download latest build](https://nightly.link/usatiuk/dhfs/workflows/server/main/Run%20wrapper.zip)

-This is a simple wrapper around the jar/web ui distribution that allows you to run/stop
-the DHFS server in the background, and update itself (hopefully!)
+This is a simple set of scripts that allows you to run/stop
+the DHFS server in the background, and update it.
+
+Once unpacked, in the root folder (`dhfs`), there will be 3 folders:
+
+- `app` contains the application
+- `data` contains the filesystem data storage
+- `fuse` is the default filesystem mount point (not on Windows, the default mount drive letter is `Z`)
+
+Note that on Windows, the path to the root can not contain spaces.

 ## How to use it?

+### General prerequisites

-Unpack the run-wrapper and run the `run` script. The filesystem should be mounted to the `fuse` folder in the run-wrapper root directory.
+Java should be available as `java` in `PATH`, or with a correctly set `JAVA_HOME` (ignored on Windows), and Java 21 is required.

-Then, a web interface will be available at `losthost:8080`, that can be used to connect with other peers.
+FUSE 2 userspace library also should be available:
+
+- On Ubuntu `libfuse2` package can be installed, or an analogous package for other distributions.
+
+- On Windows, [WinFsp](https://winfsp.dev/) should be installed.
+
+- On macOS, [macFUSE](https://macfuse.github.io/).
+
+### How to run it?
+
+In the run-wrapper `app` folder, 3 scripts are available.
+
+- `run` script starts the filesystem
+- `stop` script stops it
+- `update` script will update the filesystem to the newest available CI build
+
+On Windows, Powershell versions of the scripts should be used. For them to work, it might be required to allow execution of unsigned scripts using `set-executionpolicy unrestricted`.
+
+### Additional options
+
+Additional options for the filesystem can be specified in the `extra-opts` file in the same directory with the run scripts.
+
+One line in the `extra-opts` file corresponds to one option passed to the JVM when starting the filesystem.
+
+Some extra possible configuration options are:
+
+- `-Ddhfs.fuse.root=` specifies the root where filesystem should be mounted. By default, it is the `fuse` path under the `run-wrapper` root. For windows, it should be a disk root, by default `Z:\`.
+- `-Ddhfs.objects.last-seen.timeout=` specifies the period of time (in seconds) after which unavailable peers will be ignored for garbage collection and resynchronized after being reconnected. The default is 43200 (30 days), if set to `-1`, this feature is disabled.
+- `-Ddhfs.objects.autosync.download-all=` specifies whether all objects (files and their data) should be downloaded to this peer. `true` or `false`, the default is `false`.
+- `-Ddhfs.objects.peerdiscovery.port=` port to broadcast on and listen to for LAN peer discovery (default is `42262`)
+- `-Ddhfs.objects.peerdiscovery.broadcast=` whether to enable local peer discovery or not (default is `true`)
+- `-Dquarkus.http.port=` HTTP port to listen on (default is `8080`)
+- `-Dquarkus.http.ssl-port=` HTTPS port to listen on (default is `8443`)
+- `-Dquarkus.http.host=` IP address to listen on (default is `0.0.0.0`)
+- `-Ddhfs.peerdiscovery.static-peers=` allows to manually specify a peer's address in format of `peer id:http port:https port`, for example `-Ddhfs.peerdiscovery.static-peers=11000000-0000-0000-0000-000000000000:127.0.0.1:9010:9011`
+
+On Windows, the entire space for the filesystem should also be preallocated, the `-Ddhfs.objects.persistence.lmdb.size=` option controls the size (the value is in bytes), on Windows the default is 100 GB.
+
+In case of errors, the standard output is redirected to `quarkus.log` in the `app` folder, on Windows the error output is separate.
+
+### How to connect to other peers?
+
+Then, a web interface will be available at `losthost:8080` (or whatever the HTTP port is), that can be used to connect with other peers. Peers on local network should be available to be connected to automatically.
+
+## Other notes
+
+### Running tests
+
+To run LazyFS tests, LazyFS needs to be built: the git submodules need to be cloned and `./thirdparty/lazyfs/build.sh` script needs to be run. 
+
+LazyFS tests were only tested on Linux.
+
+
+### Notice
+
+This software was developed with the support of the Faculty of Information Technology, Czech Technical University in Prague, [fit.cvut.cz](https://fit.cvut.cz)
+
+<img src="./docs/logo-fit-en-cerna.svg" height="64">
--- a/dhfs-parent/.run/Main
+++ b/dhfs-parent/.run/Main
@@ -2,7 +2,7 @@
  <configuration default="false" name="Main 2" type="QsApplicationConfigurationType" factoryName="QuarkusApplication">
    <option name="MAIN_CLASS_NAME" value="com.usatiuk.dhfsfuse.Main" />
    <module name="dhfs-fuse" />
-    <option name="VM_PARAMETERS" value="-XX:+UnlockDiagnosticVMOptions -XX:+UseParallelGC -XX:+DebugNonSafepoints --enable-preview --add-exports java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED --add-exports java.base/jdk.internal.access=ALL-UNNAMED -ea -Xmx512M -Ddhfs.webui.root=$ProjectFileDir$/../webui/dist -Ddhfs.fuse.root=${HOME}/dhfs_test/2/fuse -Ddhfs.objects.persistence.files.root=${HOME}/dhfs_test/2/data -Ddhfs.objects.persistence.stuff.root=${HOME}/dhfs_test/2/data/stuff -Ddhfs.objects.peerdiscovery.broadcast=false -Dquarkus.http.port=9020 -Dquarkus.http.ssl-port=9021 -Ddhfs.peerdiscovery.preset-uuid=22000000-0000-0000-0000-000000000000 -Ddhfs.peerdiscovery.static-peers=11000000-0000-0000-0000-000000000000:127.0.0.1:9010:9011" />
+    <option name="VM_PARAMETERS" value="-XX:+UnlockDiagnosticVMOptions -XX:+UseParallelGC -XX:+DebugNonSafepoints --enable-preview --add-exports java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED --add-exports java.base/jdk.internal.access=ALL-UNNAMED -ea -Xmx512M -Ddhfs.webui.root=$ProjectFileDir$/../webui/dist -Ddhfs.fuse.root=${HOME}/dhfs_test/2/fuse -Ddhfs.objects.persistence.root=${HOME}/dhfs_test/2/data -Ddhfs.objects.peerdiscovery.broadcast=false -Dquarkus.http.port=9020 -Dquarkus.http.ssl-port=9021 -Ddhfs.peerdiscovery.preset-uuid=22000000-0000-0000-0000-000000000000 -Ddhfs.peerdiscovery.static-peers=11000000-0000-0000-0000-000000000000:127.0.0.1:9010:9011" />
    <extension name="coverage">
      <pattern>
        <option name="PATTERN" value="com.usatiuk.dhfs.remoteobj.*" />
--- a/dhfs-parent/.run/Main.run.xml
+++ b/dhfs-parent/.run/Main.run.xml
@@ -2,7 +2,7 @@
  <configuration default="false" name="Main" type="QsApplicationConfigurationType" factoryName="QuarkusApplication" nameIsGenerated="true">
    <option name="MAIN_CLASS_NAME" value="com.usatiuk.dhfsfuse.Main" />
    <module name="dhfs-fuse" />
-    <option name="VM_PARAMETERS" value="-XX:+UnlockDiagnosticVMOptions -XX:+UseZGC -XX:+ZGenerational --enable-preview -XX:+DebugNonSafepoints --add-exports java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED --add-exports java.base/jdk.internal.access=ALL-UNNAMED -ea -Xmx1G -Ddhfs.webui.root=$ProjectFileDir$/../webui/dist -Ddhfs.fuse.root=${HOME}/dhfs_test/1/fuse -Ddhfs.objects.persistence.files.root=${HOME}/dhfs_test/1/data -Ddhfs.objects.persistence.stuff.root=${HOME}/dhfs_test/1/data/stuff -Ddhfs.objects.peerdiscovery.broadcast=true -Dquarkus.http.port=9010 -Dquarkus.http.ssl-port=9011 -Ddhfs.peerdiscovery.preset-uuid=11000000-0000-0000-0000-000000000000 -Ddhfs.peerdiscovery.static-peers=22000000-0000-0000-0000-000000000000:127.0.0.1:9020:9021 -Dquarkus.http.host=0.0.0.0" />
+    <option name="VM_PARAMETERS" value="-XX:+UnlockDiagnosticVMOptions -XX:+UseZGC -XX:+ZGenerational --enable-preview -XX:+DebugNonSafepoints --add-exports java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED --add-exports java.base/jdk.internal.access=ALL-UNNAMED -ea -Xmx1G -Ddhfs.webui.root=$ProjectFileDir$/../webui/dist -Ddhfs.fuse.root=${HOME}/dhfs_test/1/fuse -Ddhfs.objects.persistence.root=${HOME}/dhfs_test/1/data -Ddhfs.objects.peerdiscovery.broadcast=true -Dquarkus.http.port=9010 -Dquarkus.http.ssl-port=9011 -Ddhfs.peerdiscovery.preset-uuid=11000000-0000-0000-0000-000000000000 -Ddhfs.peerdiscovery.static-peers=22000000-0000-0000-0000-000000000000:127.0.0.1:9020:9021 -Dquarkus.http.host=0.0.0.0" />
    <extension name="coverage">
      <pattern>
        <option name="PATTERN" value="com.usatiuk.dhfs.remoteobj.*" />
--- a/dhfs-parent/dhfs-fs/docker-compose.yml
+++ b/dhfs-parent/dhfs-fs/docker-compose.yml
@@ -1,43 +0,0 @@
-version: "3.2"
-
-services:
-  dhfs1:
-    build: .
-    privileged: true
-    devices:
-      - /dev/fuse
-    volumes:
-      - $HOME/dhfs/dhfs1:/dhfs_root
-      - $HOME/dhfs/dhfs1_f:/dhfs_root/fuse:rshared
-      - ./target/quarkus-app:/app
-    command: "java --add-exports java.base/sun.nio.ch=ALL-UNNAMED
-     -Ddhfs.objects.persistence.files.root=/dhfs_root/p 
-     -Ddhfs.objects.root=/dhfs_root/d 
-     -Ddhfs.fuse.root=/dhfs_root/fuse -Dquarkus.http.host=0.0.0.0 
-     -agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=*:5005
-     -jar /app/quarkus-run.jar"
-    ports:
-      - 8080:8080
-      - 8081:8443
-      - 5005:5005
-  dhfs2:
-    build: .
-    privileged: true
-    devices:
-      - /dev/fuse
-    volumes:
-      - $HOME/dhfs/dhfs2:/dhfs_root
-      - $HOME/dhfs/dhfs2_f:/dhfs_root/fuse:rshared
-      - ./target/quarkus-app:/app
-    command: "java --add-exports java.base/sun.nio.ch=ALL-UNNAMED
-     --add-exports java.base/jdk.internal.access=ALL-UNNAMED
-     --add-opens=java.base/java.nio=ALL-UNNAMED
-     -Ddhfs.objects.persistence.files.root=/dhfs_root/p 
-     -Ddhfs.objects.root=/dhfs_root/d 
-     -Ddhfs.fuse.root=/dhfs_root/fuse -Dquarkus.http.host=0.0.0.0
-     -agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=*:5010
-     -jar /app/quarkus-run.jar"
-    ports:
-      - 8090:8080
-      - 8091:8443
-      - 5010:5010
--- a/dhfs-parent/dhfs-fs/pom.xml
+++ b/dhfs-parent/dhfs-fs/pom.xml
@@ -23,22 +23,10 @@
            <artifactId>awaitility</artifactId>
            <scope>test</scope>
        </dependency>
-        <dependency>
-            <groupId>org.bouncycastle</groupId>
-            <artifactId>bcprov-jdk18on</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.bouncycastle</groupId>
-            <artifactId>bcpkix-jdk18on</artifactId>
-        </dependency>
        <dependency>
            <groupId>io.quarkus</groupId>
            <artifactId>quarkus-security</artifactId>
        </dependency>
-        <dependency>
-            <groupId>net.openhft</groupId>
-            <artifactId>zero-allocation-hashing</artifactId>
-        </dependency>
        <dependency>
            <groupId>io.quarkus</groupId>
            <artifactId>quarkus-grpc</artifactId>
@@ -47,22 +35,6 @@
            <groupId>io.quarkus</groupId>
            <artifactId>quarkus-arc</artifactId>
        </dependency>
-        <dependency>
-            <groupId>io.quarkus</groupId>
-            <artifactId>quarkus-rest</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>io.quarkus</groupId>
-            <artifactId>quarkus-rest-client</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>io.quarkus</groupId>
-            <artifactId>quarkus-rest-client-jsonb</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>io.quarkus</groupId>
-            <artifactId>quarkus-rest-jsonb</artifactId>
-        </dependency>
        <dependency>
            <groupId>io.quarkus</groupId>
            <artifactId>quarkus-scheduler</artifactId>
@@ -85,10 +57,6 @@
            <artifactId>slf4j-jboss-logmanager</artifactId>
            <scope>test</scope>
        </dependency>
-        <dependency>
-            <groupId>commons-codec</groupId>
-            <artifactId>commons-codec</artifactId>
-        </dependency>
        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-collections4</artifactId>
@@ -97,11 +65,6 @@
            <groupId>org.pcollections</groupId>
            <artifactId>pcollections</artifactId>
        </dependency>
-        <dependency>
-            <groupId>org.apache.commons</groupId>
-            <artifactId>commons-math3</artifactId>
-            <version>3.6.1</version>
-        </dependency>
        <dependency>
            <groupId>com.usatiuk.dhfs</groupId>
            <artifactId>sync-base</artifactId>
--- a/dhfs-parent/dhfs-fs/src/main/java/com/usatiuk/dhfsfs/objects/File.java
+++ b/dhfs-parent/dhfs-fs/src/main/java/com/usatiuk/dhfsfs/objects/File.java
@@ -11,10 +11,11 @@ import java.util.Set;

 /**
 * File is a data structure that represents a file in the file system
- * @param key unique key
- * @param mode file mode
- * @param cTime creation time
- * @param mTime modification time
+ *
+ * @param key     unique key
+ * @param mode    file mode
+ * @param cTime   inode modification time
+ * @param mTime   modification time
 * @param symlink true if the file is a symlink, false otherwise
 */
 public record File(JObjectKey key, long mode, long cTime, long mTime,
@@ -40,6 +41,10 @@ public record File(JObjectKey key, long mode, long cTime, long mTime,
        return new File(key, mode, cTime, System.currentTimeMillis(), symlink);
    }

+    public File withCurrentCTime() {
+        return new File(key, mode, System.currentTimeMillis(), mTime, symlink);
+    }
+
    @Override
    public Collection<JObjectKey> collectRefsTo() {
        return Set.of();
--- a/dhfs-parent/dhfs-fs/src/main/java/com/usatiuk/dhfsfs/service/DhfsFileService.java
+++ b/dhfs-parent/dhfs-fs/src/main/java/com/usatiuk/dhfsfs/service/DhfsFileService.java
@@ -19,6 +19,7 @@ import com.usatiuk.dhfsfs.objects.JKleppmannTreeNodeMetaFile;
 import com.usatiuk.objects.JData;
 import com.usatiuk.objects.JObjectKey;
 import com.usatiuk.objects.iterators.IteratorStart;
+import com.usatiuk.objects.stores.ObjectPersistentStore;
 import com.usatiuk.objects.transaction.Transaction;
 import com.usatiuk.objects.transaction.TransactionManager;
 import com.usatiuk.utils.StatusRuntimeExceptionNoStacktrace;
@@ -44,20 +45,13 @@ import java.util.stream.StreamSupport;
 */
@ApplicationScoped
 public class DhfsFileService {
-    @ConfigProperty(name = "dhfs.files.target_chunk_alignment")
+    @ConfigProperty(name = "dhfs.files.target_chunk_alignment", defaultValue = "17")
    int targetChunkAlignment;
-    @ConfigProperty(name = "dhfs.files.target_chunk_size")
-    int targetChunkSize;
    @ConfigProperty(name = "dhfs.files.max_chunk_size", defaultValue = "524288")
    int maxChunkSize;
-    @ConfigProperty(name = "dhfs.files.use_hash_for_chunks")
-    boolean useHashForChunks;
    @ConfigProperty(name = "dhfs.files.allow_recursive_delete")
    boolean allowRecursiveDelete;
-    @ConfigProperty(name = "dhfs.objects.ref_verification")
-    boolean refVerification;
-    @ConfigProperty(name = "dhfs.objects.write_log")
-    boolean writeLogging;
+

    @Inject
    Transaction curTx;
@@ -69,6 +63,8 @@ public class DhfsFileService {
    JKleppmannTreeManager jKleppmannTreeManager;
    @Inject
    JMapHelper jMapHelper;
+    @Inject
+    ObjectPersistentStore objectPersistentStore;

    private JKleppmannTreeManager.JKleppmannTree getTree() {
        return jKleppmannTreeManager.getTree(JObjectKey.of("fs"), () -> new JKleppmannTreeNodeMetaDirectory(""));
@@ -86,6 +82,10 @@ public class DhfsFileService {
        return newChunk;
    }

+    int targetChunkSize() {
+        return 1 << targetChunkAlignment;
+    }
+
    void init(@Observes @Priority(500) StartupEvent event) {
        Log.info("Initializing file service");
        getTree();
@@ -107,6 +107,7 @@ public class DhfsFileService {

    /**
     * Get the attributes of a file or directory.
+     *
     * @param uuid the UUID of the file or directory
     * @return the attributes of the file or directory
     */
@@ -133,6 +134,7 @@ public class DhfsFileService {

    /**
     * Try to resolve a path to a file or directory.
+     *
     * @param name the path to resolve
     * @return the key of the file or directory, or an empty optional if it does not exist
     */
@@ -161,6 +163,7 @@ public class DhfsFileService {

    /**
     * Create a new file with the given name and mode.
+     *
     * @param name the name of the file
     * @param mode the mode of the file
     * @return the key of the created file
@@ -191,6 +194,7 @@ public class DhfsFileService {

    /**
     * Get the parent directory of a file or directory.
+     *
     * @param ino the key of the file or directory
     * @return the parent directory
     */
@@ -207,6 +211,7 @@ public class DhfsFileService {

    /**
     * Create a new directory with the given name and mode.
+     *
     * @param name the name of the directory
     * @param mode the mode of the directory
     */
@@ -227,6 +232,7 @@ public class DhfsFileService {

    /**
     * Unlink a file or directory.
+     *
     * @param name the name of the file or directory
     * @throws DirectoryNotEmptyException if the directory is not empty and recursive delete is not allowed
     */
@@ -245,11 +251,12 @@ public class DhfsFileService {

    /**
     * Rename a file or directory.
+     *
     * @param from the old name
-     * @param to the new name
+     * @param to   the new name
     * @return true if the rename was successful, false otherwise
     */
-    public Boolean rename(String from, String to) {
+    public boolean rename(String from, String to) {
        return jObjectTxManager.executeTx(() -> {
            var node = getDirEntry(from);
            JKleppmannTreeNodeMeta meta = node.meta();
@@ -265,11 +272,12 @@ public class DhfsFileService {

    /**
     * Change the mode of a file or directory.
+     *
     * @param uuid the ID of the file or directory
     * @param mode the new mode
     * @return true if the mode was changed successfully, false otherwise
     */
-    public Boolean chmod(JObjectKey uuid, long mode) {
+    public boolean chmod(JObjectKey uuid, long mode) {
        return jObjectTxManager.executeTx(() -> {
            var dent = curTx.get(JData.class, uuid).orElseThrow(() -> new StatusRuntimeExceptionNoStacktrace(Status.NOT_FOUND));

@@ -278,7 +286,7 @@ public class DhfsFileService {
            } else if (dent instanceof RemoteObjectMeta) {
                var remote = remoteTx.getData(JDataRemote.class, uuid).orElse(null);
                if (remote instanceof File f) {
-                    remoteTx.putData(f.withMode(mode).withCurrentMTime());
+                    remoteTx.putData(f.withMode(mode).withCurrentCTime());
                    return true;
                } else {
                    throw new IllegalArgumentException(uuid + " is not a file");
@@ -291,6 +299,7 @@ public class DhfsFileService {

    /**
     * Read the contents of a directory.
+     *
     * @param name the path of the directory
     * @return an iterable of the names of the files in the directory
     */
@@ -307,9 +316,10 @@ public class DhfsFileService {

    /**
     * Read the contents of a file.
+     *
     * @param fileUuid the ID of the file
-     * @param offset the offset to start reading from
-     * @param length the number of bytes to read
+     * @param offset   the offset to start reading from
+     * @param length   the number of bytes to read
     * @return the contents of the file as a ByteString
     */
    public ByteString read(JObjectKey fileUuid, long offset, int length) {
@@ -375,6 +385,7 @@ public class DhfsFileService {

    /**
     * Get the size of a file.
+     *
     * @param uuid the ID of the file
     * @return the size of the file
     */
@@ -391,6 +402,7 @@ public class DhfsFileService {

    /**
     * Get the size of a chunk.
+     *
     * @param uuid the ID of the chunk
     * @return the size of the chunk
     */
@@ -404,12 +416,13 @@ public class DhfsFileService {

    /**
     * Write data to a file.
+     *
     * @param fileUuid the ID of the file
-     * @param offset the offset to write to
-     * @param data the data to write
+     * @param offset   the offset to write to
+     * @param data     the data to write
     * @return the number of bytes written
     */
-    public Long write(JObjectKey fileUuid, long offset, ByteString data) {
+    public long write(JObjectKey fileUuid, long offset, ByteString data) {
        return jObjectTxManager.executeTx(() -> {
            if (offset < 0)
                throw new StatusRuntimeException(Status.INVALID_ARGUMENT.withDescription("Offset should be more than zero: " + offset));
@@ -483,7 +496,7 @@ public class DhfsFileService {
                    else if (targetChunkAlignment < 0)
                        end = combinedSize;
                    else
-                        end = Math.min(cur + targetChunkSize, combinedSize);
+                        end = Math.min(cur + targetChunkSize(), combinedSize);

                    var thisChunk = pendingWrites.substring(cur, end);

@@ -513,11 +526,12 @@ public class DhfsFileService {

    /**
     * Truncate a file to the given length.
+     *
     * @param fileUuid the ID of the file
-     * @param length the new length of the file
+     * @param length   the new length of the file
     * @return true if the truncate was successful, false otherwise
     */
-    public Boolean truncate(JObjectKey fileUuid, long length) {
+    public boolean truncate(JObjectKey fileUuid, long length) {
        return jObjectTxManager.executeTx(() -> {
            if (length < 0)
                throw new StatusRuntimeException(Status.INVALID_ARGUMENT.withDescription("Length should be more than zero: " + length));
@@ -608,8 +622,9 @@ public class DhfsFileService {

    /**
     * Fill the given range with zeroes.
+     *
     * @param fillStart the start of the range
-     * @param length the end of the range
+     * @param length    the end of the range
     * @param newChunks the map to store the new chunks in
     */
    private void fillZeros(long fillStart, long length, Map<Long, JObjectKey> newChunks) {
@@ -625,11 +640,11 @@ public class DhfsFileService {
            while (cur < combinedSize) {
                long end;

-                if (targetChunkSize <= 0)
+                if (targetChunkSize() <= 0)
                    end = combinedSize;
                else {
-                    if ((combinedSize - cur) > (targetChunkSize * 1.5)) {
-                        end = cur + targetChunkSize;
+                    if ((combinedSize - cur) > (targetChunkSize() * 1.5)) {
+                        end = cur + targetChunkSize();
                    } else {
                        end = combinedSize;
                    }
@@ -649,6 +664,7 @@ public class DhfsFileService {

    /**
     * Read the contents of a symlink.
+     *
     * @param uuid the ID of the symlink
     * @return the contents of the symlink as a string
     */
@@ -660,6 +676,7 @@ public class DhfsFileService {

    /**
     * Read the contents of a symlink as a ByteString.
+     *
     * @param uuid the ID of the symlink
     * @return the contents of the symlink as a ByteString
     */
@@ -672,6 +689,7 @@ public class DhfsFileService {

    /**
     * Create a symlink.
+     *
     * @param oldpath the target of the symlink
     * @param newpath the path of the symlink
     * @return the key of the created symlink
@@ -700,12 +718,12 @@ public class DhfsFileService {

    /**
     * Set the access and modification times of a file.
+     *
     * @param fileUuid the ID of the file
-     * @param atimeMs the access time in milliseconds
-     * @param mtimeMs the modification time in milliseconds
+     * @param mtimeMs  the modification time in milliseconds
     * @return true if the times were set successfully, false otherwise
     */
-    public Boolean setTimes(JObjectKey fileUuid, long atimeMs, long mtimeMs) {
+    public boolean setTimes(JObjectKey fileUuid, long mtimeMs) {
        return jObjectTxManager.executeTx(() -> {
            var dent = curTx.get(JData.class, fileUuid).orElseThrow(() -> new StatusRuntimeExceptionNoStacktrace(Status.NOT_FOUND));

@@ -715,7 +733,7 @@ public class DhfsFileService {
            } else if (dent instanceof RemoteObjectMeta) {
                var remote = remoteTx.getData(JDataRemote.class, fileUuid).orElse(null);
                if (remote instanceof File f) {
-                    remoteTx.putData(f.withCTime(atimeMs).withMTime(mtimeMs));
+                    remoteTx.putData(f.withCTime(System.currentTimeMillis()).withMTime(mtimeMs));
                    return true;
                } else {
                    throw new IllegalArgumentException(fileUuid + " is not a file");
@@ -728,6 +746,7 @@ public class DhfsFileService {

    /**
     * Get the size of a file.
+     *
     * @param fileUuid the ID of the file
     * @return the size of the file
     */
@@ -752,12 +771,31 @@ public class DhfsFileService {

    /**
     * Write data to a file.
+     *
     * @param fileUuid the ID of the file
-     * @param offset the offset to write to
-     * @param data the data to write
+     * @param offset   the offset to write to
+     * @param data     the data to write
     * @return the number of bytes written
     */
-    public Long write(JObjectKey fileUuid, long offset, byte[] data) {
+    public long write(JObjectKey fileUuid, long offset, byte[] data) {
        return write(fileUuid, offset, UnsafeByteOperations.unsafeWrap(data));
    }
+
+    /**
+     * Get the free space on the filesystem.
+     *
+     * @return the free space in bytes
+     */
+    public long getFreeSpace() {
+        return objectPersistentStore.getFreeSpace();
+    }
+
+    /**
+     * Get the total space on the filesystem.
+     *
+     * @return the total space in bytes
+     */
+    public long getTotalSpace() {
+        return objectPersistentStore.getTotalSpace();
+    }
 }
--- a/dhfs-parent/dhfs-fs/src/main/resources/application.properties
+++ b/dhfs-parent/dhfs-fs/src/main/resources/application.properties
@@ -1,7 +1,5 @@
 quarkus.grpc.server.use-separate-server=false
-dhfs.objects.peerdiscovery.port=42069
 dhfs.objects.peerdiscovery.interval=4s
-dhfs.objects.peerdiscovery.broadcast=true
 dhfs.objects.sync.timeout=30
 dhfs.objects.sync.ping.timeout=5
 dhfs.objects.invalidation.threads=16
@@ -14,16 +12,12 @@ dhfs.objects.persistence.stuff.root=${HOME}/dhfs_default/data/stuff
 dhfs.fuse.debug=false
 dhfs.fuse.enabled=true
 dhfs.files.allow_recursive_delete=false
-dhfs.files.target_chunk_size=2097152
-dhfs.files.target_chunk_alignment=19
 dhfs.objects.deletion.delay=1000
 dhfs.objects.deletion.can-delete-retry-delay=10000
 dhfs.objects.ref_verification=true
 dhfs.files.use_hash_for_chunks=false
 dhfs.objects.autosync.threads=16
 dhfs.objects.autosync.download-all=false
-dhfs.objects.move-processor.threads=16
-dhfs.objects.ref-processor.threads=16
 dhfs.objects.opsender.batch-size=100
 dhfs.objects.lock_timeout_secs=2
 dhfs.local-discovery=true
--- a/dhfs-parent/dhfs-fs/src/test/java/com/usatiuk/dhfsfs/TempDataProfile.java
+++ b/dhfs-parent/dhfs-fs/src/test/java/com/usatiuk/dhfsfs/TempDataProfile.java
@@ -21,7 +21,7 @@ abstract public class TempDataProfile implements QuarkusTestProfile {
            throw new RuntimeException(e);
        }
        var ret = new HashMap<String, String>();
-        ret.put("dhfs.objects.persistence.files.root", tempDirWithPrefix.resolve("dhfs_root_test").toString());
+        ret.put("dhfs.objects.persistence.root", tempDirWithPrefix.resolve("dhfs_root_test").toString());
        ret.put("dhfs.fuse.root", tempDirWithPrefix.resolve("dhfs_fuse_root_test").toString());
        getConfigOverrides(ret);
        return ret;
--- a/dhfs-parent/dhfs-fs/src/test/java/com/usatiuk/dhfsfs/TestDataCleaner.java
+++ b/dhfs-parent/dhfs-fs/src/test/java/com/usatiuk/dhfsfs/TestDataCleaner.java
@@ -15,7 +15,7 @@ import java.util.Objects;

@ApplicationScoped
 public class TestDataCleaner {
-    @ConfigProperty(name = "dhfs.objects.persistence.files.root")
+    @ConfigProperty(name = "dhfs.objects.persistence.root")
    String tempDirectory;

    void init(@Observes @Priority(1) StartupEvent event) throws IOException {
--- a/dhfs-parent/dhfs-fs/src/test/java/com/usatiuk/dhfsfs/benchmarks/Benchmarker.java
+++ b/dhfs-parent/dhfs-fs/src/test/java/com/usatiuk/dhfsfs/benchmarks/Benchmarker.java
@@ -1,83 +0,0 @@
-package com.usatiuk.dhfsfs.benchmarks;
-
-import io.quarkus.logging.Log;
-import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
-
-import java.util.Arrays;
-import java.util.function.Supplier;
-
-public class Benchmarker {
-    static <T> long[] runLatency(Supplier<T> fn, int iterations) {
-        var out = new long[iterations];
-
-        int hash = 1;
-
-        for (int i = 0; i < iterations; i++) {
-            long startNanos = System.nanoTime();
-            var cur = fn.get();
-            long stopNanos = System.nanoTime();
-            out[i] = stopNanos - startNanos;
-            hash = hash * 31 + cur.hashCode();
-        }
-
-        System.out.println("\nHash: " + hash);
-
-        return out;
-    }
-
-    static <T> long[] runThroughput(Supplier<T> fn, int iterations, long iterationTime) {
-        var out = new long[iterations];
-
-        int hash = 1;
-
-        for (int i = 0; i < iterations; i++) {
-            long startMillis = System.currentTimeMillis();
-            long count = 0;
-            // FIXME: That's probably janky
-            while (System.currentTimeMillis() - startMillis < iterationTime) {
-                var res = fn.get();
-                count++;
-                hash = hash * 31 + res.hashCode();
-            }
-            System.out.println("Ran iteration " + i + "/" + iterations + " count=" + count);
-            out[i] = count;
-        }
-
-        System.out.println("\nHash: " + hash);
-
-        return out;
-    }
-
-    static void printStats(double[] data, String unit) {
-        DescriptiveStatistics stats = new DescriptiveStatistics();
-        for (var r : data) {
-            stats.addValue(r);
-        }
-        Log.info("\n" + stats +
-                "\n 50%: " + stats.getPercentile(50) + " " + unit +
-                "\n 90%: " + stats.getPercentile(90) + " " + unit +
-                "\n 95%: " + stats.getPercentile(95) + " " + unit +
-                "\n 99%: " + stats.getPercentile(99) + " " + unit +
-                "\n 99.9%: " + stats.getPercentile(99.9) + " " + unit +
-                "\n 99.99%: " + stats.getPercentile(99.99) + " " + unit
-        );
-
-    }
-
-    static <T> void runAndPrintMixSimple(String name, Supplier<T> fn, int latencyIterations, int thrptIterations, int thrptIterationTime, int warmupIterations, int warmupIterationTime) {
-        System.out.println("\n=========\n" + "Running " + name + "\n=========\n");
-        System.out.println("==Warmup==");
-        runThroughput(fn, warmupIterations, warmupIterationTime);
-        System.out.println("==Warmup done==");
-        System.out.println("==Throughput==");
-        var thrpt = runThroughput(fn, thrptIterations, thrptIterationTime);
-        printStats(Arrays.stream(thrpt).mapToDouble(o -> (double) o / 1000).toArray(), "ops/s");
-        System.out.println("==Throughput done==");
-        System.out.println("==Latency==");
-        var lat = runLatency(fn, latencyIterations);
-        printStats(Arrays.stream(lat).mapToDouble(o -> (double) o).toArray(), "ns/op");
-        System.out.println("==Latency done==");
-        System.out.println("\n=========\n" + name + " done" + "\n=========\n");
-    }
-
-}
--- a/dhfs-parent/dhfs-fs/src/test/java/com/usatiuk/dhfsfs/benchmarks/DhfsFileBenchmarkTest.java
+++ b/dhfs-parent/dhfs-fs/src/test/java/com/usatiuk/dhfsfs/benchmarks/DhfsFileBenchmarkTest.java
@@ -1,53 +0,0 @@
-package com.usatiuk.dhfsfs.benchmarks;
-
-import com.google.protobuf.UnsafeByteOperations;
-import com.usatiuk.dhfsfs.TempDataProfile;
-import com.usatiuk.dhfsfs.service.DhfsFileService;
-import com.usatiuk.objects.JObjectKey;
-import io.quarkus.test.junit.QuarkusTest;
-import io.quarkus.test.junit.TestProfile;
-import jakarta.inject.Inject;
-import org.junit.jupiter.api.Disabled;
-import org.junit.jupiter.api.Test;
-
-import java.nio.ByteBuffer;
-import java.util.Map;
-
-class Profiles {
-    public static class DhfsFuseTestProfile extends TempDataProfile {
-        @Override
-        protected void getConfigOverrides(Map<String, String> ret) {
-            ret.put("quarkus.log.category.\"com.usatiuk.dhfs\".level", "INFO");
-            ret.put("dhfs.fuse.enabled", "false");
-            ret.put("dhfs.objects.ref_verification", "false");
-        }
-    }
-}
-
-@QuarkusTest
-@TestProfile(Profiles.DhfsFuseTestProfile.class)
-public class DhfsFileBenchmarkTest {
-    @Inject
-    DhfsFileService dhfsFileService;
-
-    @Test
-    @Disabled
-    void openRootTest() {
-        Benchmarker.runAndPrintMixSimple("dhfsFileService.open(\"\")",
-                () -> {
-                    return dhfsFileService.open("");
-                }, 1_000_000, 5, 1000, 5, 1000);
-    }
-
-    @Test
-    @Disabled
-    void writeMbTest() {
-        JObjectKey file = dhfsFileService.create("/writeMbTest", 0777).get();
-        var bb = ByteBuffer.allocateDirect(1024 * 1024);
-        Benchmarker.runAndPrintMixSimple("dhfsFileService.write(\"\")",
-                () -> {
-                    var thing = UnsafeByteOperations.unsafeWrap(bb);
-                    return dhfsFileService.write(file, dhfsFileService.size(file), thing);
-                }, 1_000, 10, 100, 1, 100);
-    }
-}
--- a/dhfs-parent/dhfs-fs/src/test/resources/application.properties
+++ b/dhfs-parent/dhfs-fs/src/test/resources/application.properties
@@ -1,5 +1,4 @@
-dhfs.objects.persistence.files.root=${HOME}/dhfs_data/dhfs_root_test
-dhfs.objects.root=${HOME}/dhfs_data/dhfs_root_d_test
+dhfs.objects.persistence.root=${HOME}/dhfs_data/dhfs_root_test
 dhfs.fuse.root=${HOME}/dhfs_data/dhfs_fuse_root_test
 dhfs.objects.ref_verification=true
 dhfs.objects.deletion.delay=0
--- a/dhfs-parent/dhfs-fuse/docker-compose.yml
+++ b/dhfs-parent/dhfs-fuse/docker-compose.yml
@@ -11,8 +11,7 @@ services:
      - $HOME/dhfs/dhfs1_f:/dhfs_root/fuse:rshared
      - ./target/quarkus-app:/app
    command: "java --add-exports java.base/sun.nio.ch=ALL-UNNAMED
-     -Ddhfs.objects.persistence.files.root=/dhfs_root/p 
-     -Ddhfs.objects.root=/dhfs_root/d 
+     -Ddhfs.objects.persistence.root=/dhfs_root/p 
     -Ddhfs.fuse.root=/dhfs_root/fuse -Dquarkus.http.host=0.0.0.0 
     -agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=*:5005
     -jar /app/quarkus-run.jar"
@@ -32,8 +31,7 @@ services:
    command: "java --add-exports java.base/sun.nio.ch=ALL-UNNAMED
     --add-exports java.base/jdk.internal.access=ALL-UNNAMED
     --add-opens=java.base/java.nio=ALL-UNNAMED
-     -Ddhfs.objects.persistence.files.root=/dhfs_root/p 
-     -Ddhfs.objects.root=/dhfs_root/d 
+     -Ddhfs.objects.persistence.root=/dhfs_root/p 
     -Ddhfs.fuse.root=/dhfs_root/fuse -Dquarkus.http.host=0.0.0.0
     -agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=*:5010
     -jar /app/quarkus-run.jar"
--- a/dhfs-parent/dhfs-fuse/pom.xml
+++ b/dhfs-parent/dhfs-fuse/pom.xml
@@ -23,22 +23,10 @@
            <artifactId>awaitility</artifactId>
            <scope>test</scope>
        </dependency>
-        <dependency>
-            <groupId>org.bouncycastle</groupId>
-            <artifactId>bcprov-jdk18on</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.bouncycastle</groupId>
-            <artifactId>bcpkix-jdk18on</artifactId>
-        </dependency>
        <dependency>
            <groupId>io.quarkus</groupId>
            <artifactId>quarkus-security</artifactId>
        </dependency>
-        <dependency>
-            <groupId>net.openhft</groupId>
-            <artifactId>zero-allocation-hashing</artifactId>
-        </dependency>
        <dependency>
            <groupId>io.quarkus</groupId>
            <artifactId>quarkus-grpc</artifactId>
@@ -47,14 +35,6 @@
            <groupId>io.quarkus</groupId>
            <artifactId>quarkus-arc</artifactId>
        </dependency>
-        <dependency>
-            <groupId>io.quarkus</groupId>
-            <artifactId>quarkus-rest</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>io.quarkus</groupId>
-            <artifactId>quarkus-rest-client</artifactId>
-        </dependency>
        <dependency>
            <groupId>io.quarkus</groupId>
            <artifactId>quarkus-rest-client-jsonb</artifactId>
@@ -90,10 +70,6 @@
            <artifactId>slf4j-jboss-logmanager</artifactId>
            <scope>test</scope>
        </dependency>
-        <dependency>
-            <groupId>commons-codec</groupId>
-            <artifactId>commons-codec</artifactId>
-        </dependency>
        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-collections4</artifactId>
@@ -102,11 +78,6 @@
            <groupId>org.pcollections</groupId>
            <artifactId>pcollections</artifactId>
        </dependency>
-        <dependency>
-            <groupId>org.apache.commons</groupId>
-            <artifactId>commons-math3</artifactId>
-            <version>3.6.1</version>
-        </dependency>
        <dependency>
            <groupId>com.usatiuk.dhfs</groupId>
            <artifactId>dhfs-fs</artifactId>
@@ -139,7 +110,7 @@
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-failsafe-plugin</artifactId>
                <configuration>
-                    <forkCount>0.5C</forkCount>
+                    <forkCount>1C</forkCount>
                    <reuseForks>false</reuseForks>
                    <parallel>classes</parallel>
                    <systemPropertyVariables>
--- a/dhfs-parent/dhfs-fuse/src/main/java/com/usatiuk/dhfsfuse/DhfsFuse.java
+++ b/dhfs-parent/dhfs-fuse/src/main/java/com/usatiuk/dhfsfuse/DhfsFuse.java
@@ -39,6 +39,9 @@ import java.util.concurrent.atomic.AtomicLong;

 import static jnr.posix.FileStat.*;

+/**
+ * FUSE file system implementation.
+ */
@ApplicationScoped
 public class DhfsFuse extends FuseStubFS {
    private static final int blksize = 1048576;
@@ -51,11 +54,15 @@ public class DhfsFuse extends FuseStubFS {
    boolean enabled;
    @ConfigProperty(name = "dhfs.fuse.debug")
    Boolean debug;
-    @ConfigProperty(name = "dhfs.files.target_chunk_size")
-    int targetChunkSize;
    @Inject
    DhfsFileService fileService;

+    /**
+     * Allocate a handle for the given key.
+     *
+     * @param key the key to allocate a handle for
+     * @return the allocated handle, not 0
+     */
    private long allocateHandle(JObjectKey key) {
        while (true) {
            var newFh = _fh.getAndIncrement();
@@ -66,8 +73,15 @@ public class DhfsFuse extends FuseStubFS {
        }
    }

+    /**
+     * Get the key from the handle.
+     *
+     * @param handle the handle to get the key from
+     * @return the key, or null if not found
+     */
    private JObjectKey getFromHandle(long handle) {
-        assert handle != 0;
+        if (handle == 0)
+            throw new IllegalStateException("Handle is 0");
        return _openHandles.get(handle);
    }

@@ -98,7 +112,6 @@ public class DhfsFuse extends FuseStubFS {
                opts.add("-o");
                opts.add("iosize=" + iosize);
            } else if (SystemUtils.IS_OS_LINUX) {
-                // FIXME: There's something else missing: the writes still seem to be 32k max
 //            opts.add("-o");
 //            opts.add("large_read");
                opts.add("-o");
@@ -115,7 +128,9 @@ public class DhfsFuse extends FuseStubFS {
            opts.add("-o");
            opts.add("gid=" + gid);
        }
+        Log.info("FUSE options: " + opts);
        mount(Paths.get(root), false, debug, opts.toArray(String[]::new));
+        Log.info("Mounted");
    }

    void shutdown(@Observes @Priority(1) ShutdownEvent event) {
@@ -130,13 +145,12 @@ public class DhfsFuse extends FuseStubFS {
        try {
            stbuf.f_frsize.set(blksize);
            stbuf.f_bsize.set(blksize);
-            // FIXME:
-            stbuf.f_blocks.set(1024 * 1024 * 1024 / blksize); // total data blocks in file system
-            stbuf.f_bfree.set(1024 * 1024 * 1024 / blksize);  // free blocks in fs
-            stbuf.f_bavail.set(1024 * 1024 * 1024 / blksize); // avail blocks in fs
-            stbuf.f_files.set(1000); //FIXME:
-            stbuf.f_ffree.set(Integer.MAX_VALUE - 2000); //FIXME:
-            stbuf.f_favail.set(Integer.MAX_VALUE - 2000); //FIXME:
+            stbuf.f_blocks.set(fileService.getTotalSpace() / blksize); // total data blocks in file system
+            stbuf.f_bfree.set(fileService.getFreeSpace() / blksize);  // free blocks in fs
+            stbuf.f_bavail.set(fileService.getFreeSpace() / blksize); // avail blocks in fs
+            stbuf.f_files.set(1000); // TODO: Calculate real file counts?
+            stbuf.f_ffree.set(Integer.MAX_VALUE - 1000);
+            stbuf.f_favail.set(Integer.MAX_VALUE - 1000);
            stbuf.f_namemax.set(2048);
            return super.statfs(path, stbuf);
        } catch (Throwable e) {
@@ -172,13 +186,13 @@ public class DhfsFuse extends FuseStubFS {
                }
            }

-            // FIXME: Race?
            stat.st_ctim.tv_sec.set(found.get().ctime() / 1000);
            stat.st_ctim.tv_nsec.set((found.get().ctime() % 1000) * 1000);
            stat.st_mtim.tv_sec.set(found.get().mtime() / 1000);
            stat.st_mtim.tv_nsec.set((found.get().mtime() % 1000) * 1000);
-            stat.st_atim.tv_sec.set(found.get().mtime() / 1000);
-            stat.st_atim.tv_nsec.set((found.get().mtime() % 1000) * 1000);
+            var atime = Math.max(found.get().ctime(), found.get().mtime());
+            stat.st_atim.tv_sec.set(atime / 1000);
+            stat.st_atim.tv_nsec.set((atime % 1000) * 1000000L);
            stat.st_blksize.set(blksize);
        } catch (Throwable e) {
            Log.error("When getattr " + path, e);
@@ -194,8 +208,7 @@ public class DhfsFuse extends FuseStubFS {
            if (fileOpt.isEmpty()) return -ErrorCodes.ENOENT();
            var file = fileOpt.get();
            var res = fileService.setTimes(file,
-                    timespec[0].tv_sec.get() * 1000,
-                    timespec[1].tv_sec.get() * 1000);
+                    timespec[1].tv_sec.get() * 1000L + timespec[1].tv_nsec.longValue() / 1000000L);
            if (!res) return -ErrorCodes.EINVAL();
            else return 0;
        } catch (Throwable e) {
@@ -256,7 +269,7 @@ public class DhfsFuse extends FuseStubFS {
        try {
            var fileKey = getFromHandle(fi.fh.get());
            var written = fileService.write(fileKey, offset, UnsafeByteOperations.unsafeWrap(buffer));
-            return written.intValue();
+            return Math.toIntExact(written);
        } catch (Exception e) {
            Log.error("When writing " + path, e);
            return -ErrorCodes.EIO();
--- a/dhfs-parent/dhfs-fuse/src/main/java/com/usatiuk/dhfsfuse/JnrPtrByteOutput.java
+++ b/dhfs-parent/dhfs-fuse/src/main/java/com/usatiuk/dhfsfuse/JnrPtrByteOutput.java
@@ -7,6 +7,9 @@ import jnr.ffi.Pointer;
 import java.nio.ByteBuffer;
 import java.nio.MappedByteBuffer;

+/**
+ * JnrPtrByteOutput is a ByteOutput implementation that writes to a `jnr.ffi.Pointer`.
+ */
 public class JnrPtrByteOutput extends ByteOutput {
    private final Pointer _backing;
    private final long _size;
--- a/dhfs-parent/dhfs-fuse/src/main/resources/application.properties
+++ b/dhfs-parent/dhfs-fuse/src/main/resources/application.properties
@@ -1,32 +1,19 @@
 quarkus.grpc.server.use-separate-server=false
-dhfs.objects.peerdiscovery.port=42069
 dhfs.objects.peerdiscovery.interval=4s
-dhfs.objects.peerdiscovery.broadcast=true
 dhfs.objects.sync.timeout=30
 dhfs.objects.sync.ping.timeout=5
 dhfs.objects.invalidation.threads=16
 dhfs.objects.invalidation.delay=1000
-dhfs.objects.reconnect_interval=5s
-dhfs.objects.write_log=false
-dhfs.objects.periodic-push-op-interval=5m
 dhfs.fuse.root=${HOME}/dhfs_default/fuse
 dhfs.objects.persistence.stuff.root=${HOME}/dhfs_default/data/stuff
 dhfs.fuse.debug=false
 dhfs.fuse.enabled=true
 dhfs.files.allow_recursive_delete=false
-dhfs.files.target_chunk_size=524288
-dhfs.files.max_chunk_size=524288
-dhfs.files.target_chunk_alignment=17
 dhfs.objects.deletion.delay=1000
 dhfs.objects.deletion.can-delete-retry-delay=10000
 dhfs.objects.ref_verification=true
-dhfs.files.use_hash_for_chunks=false
-dhfs.objects.autosync.threads=16
+dhfs.objects.autosync.threads=8
 dhfs.objects.autosync.download-all=false
-dhfs.objects.move-processor.threads=16
-dhfs.objects.ref-processor.threads=16
-dhfs.objects.opsender.batch-size=100
-dhfs.objects.lock_timeout_secs=2
 dhfs.local-discovery=true
 dhfs.peerdiscovery.timeout=10000
 quarkus.log.category."com.usatiuk".min-level=TRACE
--- a/dhfs-parent/dhfs-fuse/src/test/java/com/usatiuk/dhfsfuse/TempDataProfile.java
+++ b/dhfs-parent/dhfs-fuse/src/test/java/com/usatiuk/dhfsfuse/TempDataProfile.java
@@ -21,7 +21,7 @@ abstract public class TempDataProfile implements QuarkusTestProfile {
            throw new RuntimeException(e);
        }
        var ret = new HashMap<String, String>();
-        ret.put("dhfs.objects.persistence.files.root", tempDirWithPrefix.resolve("dhfs_root_test").toString());
+        ret.put("dhfs.objects.persistence.root", tempDirWithPrefix.resolve("dhfs_root_test").toString());
        ret.put("dhfs.fuse.root", tempDirWithPrefix.resolve("dhfs_fuse_root_test").toString());
        getConfigOverrides(ret);
        return ret;
--- a/dhfs-parent/dhfs-fuse/src/test/java/com/usatiuk/dhfsfuse/TestDataCleaner.java
+++ b/dhfs-parent/dhfs-fuse/src/test/java/com/usatiuk/dhfsfuse/TestDataCleaner.java
@@ -15,7 +15,7 @@ import java.util.Objects;

@ApplicationScoped
 public class TestDataCleaner {
-    @ConfigProperty(name = "dhfs.objects.persistence.files.root")
+    @ConfigProperty(name = "dhfs.objects.persistence.root")
    String tempDirectory;

    void init(@Observes @Priority(1) StartupEvent event) throws IOException {
--- a/dhfs-parent/dhfs-fuse/src/test/java/com/usatiuk/dhfsfuse/integration/DhfsFuseIT.java
+++ b/dhfs-parent/dhfs-fuse/src/test/java/com/usatiuk/dhfsfuse/integration/DhfsFuseIT.java
@@ -10,10 +10,8 @@ import org.testcontainers.containers.GenericContainer;
 import org.testcontainers.containers.Network;
 import org.testcontainers.containers.output.Slf4jLogConsumer;
 import org.testcontainers.containers.output.WaitingConsumer;
-import org.testcontainers.containers.wait.strategy.Wait;

 import java.io.IOException;
-import java.time.Duration;
 import java.util.Objects;
 import java.util.UUID;
 import java.util.concurrent.TimeUnit;
@@ -40,11 +38,11 @@ public class DhfsFuseIT {
        container1 = new GenericContainer<>(DhfsImage.getInstance())
                .withPrivilegedMode(true)
                .withCreateContainerCmdModifier(cmd -> Objects.requireNonNull(cmd.getHostConfig()).withDevices(Device.parse("/dev/fuse")))
-                .waitingFor(Wait.forLogMessage(".*Listening.*", 1).withStartupTimeout(Duration.ofSeconds(60))).withNetwork(network);
+                .withNetwork(network);
        container2 = new GenericContainer<>(DhfsImage.getInstance())
                .withPrivilegedMode(true)
                .withCreateContainerCmdModifier(cmd -> Objects.requireNonNull(cmd.getHostConfig()).withDevices(Device.parse("/dev/fuse")))
-                .waitingFor(Wait.forLogMessage(".*Listening.*", 1).withStartupTimeout(Duration.ofSeconds(60))).withNetwork(network);
+                .withNetwork(network);

        Stream.of(container1, container2).parallel().forEach(GenericContainer::start);

@@ -55,8 +53,11 @@ public class DhfsFuseIT {
        var loggingConsumer2 = new Slf4jLogConsumer(LoggerFactory.getLogger(DhfsFuseIT.class)).withPrefix("2-" + testInfo.getDisplayName());
        container2.followOutput(loggingConsumer2.andThen(waitingConsumer2));

-        c1uuid = container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
-        c2uuid = container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
+        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Listening"), 60, TimeUnit.SECONDS);
+        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Listening"), 60, TimeUnit.SECONDS);
+
+        c1uuid = container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/self_uuid").getStdout();
+        c2uuid = container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/self_uuid").getStdout();

        Assertions.assertDoesNotThrow(() -> UUID.fromString(c1uuid));
        Assertions.assertDoesNotThrow(() -> UUID.fromString(c2uuid));
@@ -128,13 +129,15 @@ public class DhfsFuseIT {
                "tesempty\n".equals(container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/fuse/testf1").getStdout()));

        var client = DockerClientFactory.instance().client();
-        client.pauseContainerCmd(container2.getContainerId()).exec();
+        client.disconnectFromNetworkCmd().withContainerId(container2.getContainerId()).withNetworkId(network.getId()).exec();
+        client.disconnectFromNetworkCmd().withContainerId(container1.getContainerId()).withNetworkId(network.getId()).exec();

        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Lost connection to"), 60, TimeUnit.SECONDS);

        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container1.execInContainer("/bin/sh", "-c", "echo newfile > /dhfs_test/fuse/testf2").getExitCode());

-        client.unpauseContainerCmd(container2.getContainerId()).exec();
+        client.connectToNetworkCmd().withContainerId(container2.getContainerId()).withNetworkId(network.getId()).exec();
+        client.connectToNetworkCmd().withContainerId(container1.getContainerId()).withNetworkId(network.getId()).exec();

        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Connected"), 60, TimeUnit.SECONDS);
        await().atMost(45, TimeUnit.SECONDS).until(() ->
@@ -152,13 +155,13 @@ public class DhfsFuseIT {
                "tesempty\n".equals(container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/fuse/testf1").getStdout()));

        var client = DockerClientFactory.instance().client();
-        client.pauseContainerCmd(container2.getContainerId()).exec();
+        client.disconnectFromNetworkCmd().withNetworkId(network.getId()).withContainerId(container2.getContainerId()).exec();

        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Lost connection to"), 60, TimeUnit.SECONDS);

        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container1.execInContainer("/bin/sh", "-c", "echo rewritten > /dhfs_test/fuse/testf1").getExitCode());

-        client.unpauseContainerCmd(container2.getContainerId()).exec();
+        client.connectToNetworkCmd().withContainerId(container2.getContainerId()).withNetworkId(network.getId()).exec();

        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Connected"), 60, TimeUnit.SECONDS);

@@ -200,18 +203,34 @@ public class DhfsFuseIT {
        await().atMost(45, TimeUnit.SECONDS).until(() ->
                "tesempty\n".equals(container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/fuse/testf1").getStdout()));

-        container2.stop();
+        var client = DockerClientFactory.instance().client();
+        client.disconnectFromNetworkCmd().withNetworkId(network.getId()).withContainerId(container2.getContainerId()).exec();
        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("kicked"), 60, TimeUnit.SECONDS, 1);

+        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container1.execInContainer("/bin/sh", "-c", "echo tesempty2 > /dhfs_test/fuse/testf2").getExitCode());
+        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container2.execInContainer("/bin/sh", "-c", "echo tesempty3 > /dhfs_test/fuse/testf3").getExitCode());
+
        Log.info("Deleting");
        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container1.execInContainer("/bin/sh", "-c", "rm /dhfs_test/fuse/testf1").getExitCode());
        Log.info("Deleted");

-        // FIXME?
        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Deleting from persistent"), 60, TimeUnit.SECONDS, 3);

+        client.connectToNetworkCmd().withContainerId(container2.getContainerId()).withNetworkId(network.getId()).exec();
+
+        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Connected"), 60, TimeUnit.SECONDS);
+
        await().atMost(45, TimeUnit.SECONDS).until(() ->
                1 == container1.execInContainer("/bin/sh", "-c", "test -f /dhfs_test/fuse/testf1").getExitCode());
+
+        await().atMost(45, TimeUnit.SECONDS).until(() ->
+                "tesempty2\n".equals(container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/fuse/testf2").getStdout()));
+        await().atMost(45, TimeUnit.SECONDS).until(() ->
+                "tesempty3\n".equals(container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/fuse/testf3").getStdout()));
+        await().atMost(45, TimeUnit.SECONDS).until(() ->
+                "tesempty2\n".equals(container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/fuse/testf2").getStdout()));
+        await().atMost(45, TimeUnit.SECONDS).until(() ->
+                "tesempty3\n".equals(container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/fuse/testf3").getStdout()));
    }

    @Test
@@ -359,12 +378,12 @@ public class DhfsFuseIT {
        });

        var client = DockerClientFactory.instance().client();
-        client.pauseContainerCmd(container1.getContainerId()).exec();
+        client.disconnectFromNetworkCmd().withContainerId(container1.getContainerId()).withNetworkId(network.getId()).exec();
+        client.disconnectFromNetworkCmd().withContainerId(container2.getContainerId()).withNetworkId(network.getId()).exec();
        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container2.execInContainer("/bin/sh", "-c", "mv /dhfs_test/fuse/a /dhfs_test/fuse/b").getExitCode());
-        client.pauseContainerCmd(container2.getContainerId()).exec();
-        client.unpauseContainerCmd(container1.getContainerId()).exec();
        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container1.execInContainer("/bin/sh", "-c", "mv /dhfs_test/fuse/b /dhfs_test/fuse/a").getExitCode());
-        client.unpauseContainerCmd(container2.getContainerId()).exec();
+        client.connectToNetworkCmd().withContainerId(container1.getContainerId()).withNetworkId(network.getId()).exec();
+        client.connectToNetworkCmd().withContainerId(container2.getContainerId()).withNetworkId(network.getId()).exec();


        await().atMost(45, TimeUnit.SECONDS).until(() -> {
@@ -398,14 +417,14 @@ public class DhfsFuseIT {
        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container2.execInContainer("/bin/sh", "-c", "ls /dhfs_test/fuse/").getExitCode());
        await().atMost(45, TimeUnit.SECONDS).until(() -> "tesempty\n".equals(container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/fuse/testf1").getStdout()));

-        client.pauseContainerCmd(container1.getContainerId()).exec();
+        client.disconnectFromNetworkCmd().withContainerId(container1.getContainerId()).withNetworkId(network.getId()).exec();
+        client.disconnectFromNetworkCmd().withContainerId(container2.getContainerId()).withNetworkId(network.getId()).exec();
+
        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Lost connection to"), 60, TimeUnit.SECONDS, 1);

        Log.info("Removing");
        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container2.execInContainer("/bin/sh", "-c", "rm /dhfs_test/fuse/testf1").getExitCode());

-        client.pauseContainerCmd(container2.getContainerId()).exec();
-        client.unpauseContainerCmd(container1.getContainerId()).exec();
        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Lost connection to"), 60, TimeUnit.SECONDS, 1);
        Log.info("Moving");
        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container1.execInContainer("/bin/sh", "-c", "mv /dhfs_test/fuse/testf1 /dhfs_test/fuse/testf2").getExitCode());
@@ -413,12 +432,14 @@ public class DhfsFuseIT {
        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container1.execInContainer("/bin/sh", "-c", "ls /dhfs_test/fuse/").getExitCode());
        Log.info("Reading");
        await().atMost(45, TimeUnit.SECONDS).until(() -> "tesempty\n".equals(container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/fuse/testf2").getStdout()));
-        client.unpauseContainerCmd(container2.getContainerId()).exec();
+
+        client.connectToNetworkCmd().withContainerId(container1.getContainerId()).withNetworkId(network.getId()).exec();
+        client.connectToNetworkCmd().withContainerId(container2.getContainerId()).withNetworkId(network.getId()).exec();

        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Connected"), 60, TimeUnit.SECONDS, 1);
        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Connected"), 60, TimeUnit.SECONDS, 1);
+
        // Either removed, or moved
-        // TODO: it always seems to be removed?
        Log.info("Reading both");
        await().atMost(45, TimeUnit.SECONDS).until(() -> {
            var ls1 = container1.execInContainer("/bin/sh", "-c", "ls /dhfs_test/fuse/");
--- a/dhfs-parent/dhfs-fuse/src/test/java/com/usatiuk/dhfsfuse/integration/DhfsFusex3IT.java
+++ b/dhfs-parent/dhfs-fuse/src/test/java/com/usatiuk/dhfsfuse/integration/DhfsFusex3IT.java
@@ -9,10 +9,8 @@ import org.testcontainers.containers.GenericContainer;
 import org.testcontainers.containers.Network;
 import org.testcontainers.containers.output.Slf4jLogConsumer;
 import org.testcontainers.containers.output.WaitingConsumer;
-import org.testcontainers.containers.wait.strategy.Wait;

 import java.io.IOException;
-import java.time.Duration;
 import java.util.List;
 import java.util.Objects;
 import java.util.UUID;
@@ -37,9 +35,6 @@ public class DhfsFusex3IT {

    Network network;

-    // This calculation is somewhat racy, so keep it hardcoded for now
-    long emptyFileCount = 9;
-
    @BeforeEach
    void setup(TestInfo testInfo) throws IOException, InterruptedException, TimeoutException {
        // TODO: Dedup
@@ -48,40 +43,43 @@ public class DhfsFusex3IT {
        container1 = new GenericContainer<>(DhfsImage.getInstance())
                .withPrivilegedMode(true)
                .withCreateContainerCmdModifier(cmd -> Objects.requireNonNull(cmd.getHostConfig()).withDevices(Device.parse("/dev/fuse")))
-                .waitingFor(Wait.forLogMessage(".*Listening.*", 1).withStartupTimeout(Duration.ofSeconds(60))).withNetwork(network);
+                .withNetwork(network);
        container2 = new GenericContainer<>(DhfsImage.getInstance())
                .withPrivilegedMode(true)
                .withCreateContainerCmdModifier(cmd -> Objects.requireNonNull(cmd.getHostConfig()).withDevices(Device.parse("/dev/fuse")))
-                .waitingFor(Wait.forLogMessage(".*Listening.*", 1).withStartupTimeout(Duration.ofSeconds(60))).withNetwork(network);
+                .withNetwork(network);
        container3 = new GenericContainer<>(DhfsImage.getInstance())
                .withPrivilegedMode(true)
                .withCreateContainerCmdModifier(cmd -> Objects.requireNonNull(cmd.getHostConfig()).withDevices(Device.parse("/dev/fuse")))
-                .waitingFor(Wait.forLogMessage(".*Listening.*", 1).withStartupTimeout(Duration.ofSeconds(60))).withNetwork(network);
-
+                .withNetwork(network);

        Stream.of(container1, container2, container3).parallel().forEach(GenericContainer::start);

-        c1uuid = container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
-        c2uuid = container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
-        c3uuid = container3.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
-
-        Log.info(container1.getContainerId() + "=" + c1uuid);
-        Log.info(container2.getContainerId() + "=" + c2uuid);
-        Log.info(container3.getContainerId() + "=" + c3uuid);
-
        waitingConsumer1 = new WaitingConsumer();
        var loggingConsumer1 = new Slf4jLogConsumer(LoggerFactory.getLogger(DhfsFusex3IT.class))
-                .withPrefix(c1uuid.substring(0, 4) + "-" + testInfo.getDisplayName());
+                .withPrefix(1 + "-" + testInfo.getDisplayName());
        container1.followOutput(loggingConsumer1.andThen(waitingConsumer1));
        waitingConsumer2 = new WaitingConsumer();
        var loggingConsumer2 = new Slf4jLogConsumer(LoggerFactory.getLogger(DhfsFusex3IT.class))
-                .withPrefix(c2uuid.substring(0, 4) + "-" + testInfo.getDisplayName());
+                .withPrefix(2 + "-" + testInfo.getDisplayName());
        container2.followOutput(loggingConsumer2.andThen(waitingConsumer2));
        waitingConsumer3 = new WaitingConsumer();
        var loggingConsumer3 = new Slf4jLogConsumer(LoggerFactory.getLogger(DhfsFusex3IT.class))
-                .withPrefix(c3uuid.substring(0, 4) + "-" + testInfo.getDisplayName());
+                .withPrefix(3 + "-" + testInfo.getDisplayName());
        container3.followOutput(loggingConsumer3.andThen(waitingConsumer3));

+        waitingConsumer3.waitUntil(frame -> frame.getUtf8String().contains("Listening"), 60, TimeUnit.SECONDS);
+        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Listening"), 60, TimeUnit.SECONDS);
+        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Listening"), 60, TimeUnit.SECONDS);
+
+        c1uuid = container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/self_uuid").getStdout();
+        c2uuid = container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/self_uuid").getStdout();
+        c3uuid = container3.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/self_uuid").getStdout();
+
+        Log.info(container1.getContainerId() + "=" + c1uuid + " = 1");
+        Log.info(container2.getContainerId() + "=" + c2uuid + " = 2");
+        Log.info(container3.getContainerId() + "=" + c3uuid + " = 3");
+
        Assertions.assertDoesNotThrow(() -> UUID.fromString(c1uuid));
        Assertions.assertDoesNotThrow(() -> UUID.fromString(c2uuid));
        Assertions.assertDoesNotThrow(() -> UUID.fromString(c3uuid));
@@ -119,17 +117,6 @@ public class DhfsFusex3IT {
        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Connected"), 60, TimeUnit.SECONDS, 2);
    }

-    private boolean checkEmpty() throws IOException, InterruptedException {
-        for (var container : List.of(container1, container2, container3)) {
-            var found = container.execInContainer("/bin/sh", "-c", "find /dhfs_test/data/objs -type f");
-            var foundWc = container.execInContainer("/bin/sh", "-c", "find /dhfs_test/data/objs -type f | wc -l");
-            Log.info("Remaining objects in " + container.getContainerId() + ": " + found.toString() + " " + foundWc.toString());
-            if (!(found.getExitCode() == 0 && foundWc.getExitCode() == 0 && Integer.parseInt(foundWc.getStdout().strip()) == emptyFileCount))
-                return false;
-        }
-        return true;
-    }
-
    @AfterEach
    void stop() {
        Stream.of(container1, container2, container3).parallel().forEach(GenericContainer::stop);
@@ -143,25 +130,6 @@ public class DhfsFusex3IT {
        await().atMost(45, TimeUnit.SECONDS).until(() -> "tesempty\n".equals(container3.execInContainer("/bin/sh", "-c", "cat /dhfs_test/fuse/testf1").getStdout()));
    }

-    // FIXME:
-    @Test
-    @Disabled
-    void largerFileDeleteTest() throws IOException, InterruptedException, TimeoutException {
-        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container1.execInContainer("/bin/sh", "-c", "cd /dhfs_test/fuse && dd if=/dev/urandom of=10MB.bin bs=1M count=10").getExitCode());
-        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container2.execInContainer("/bin/sh", "-c", "head -c 10 /dhfs_test/fuse/10MB.bin").getExitCode());
-        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container3.execInContainer("/bin/sh", "-c", "rm /dhfs_test/fuse/10MB.bin").getExitCode());
-        await().atMost(45, TimeUnit.SECONDS).until(() -> checkEmpty());
-    }
-
-    @Test
-    @Disabled
-    void largerFileDeleteTestNoDelays() throws IOException, InterruptedException, TimeoutException {
-        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container1.execInContainer("/bin/sh", "-c", "cd /dhfs_test/fuse && dd if=/dev/urandom of=10MB.bin bs=1M count=10").getExitCode());
-        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container2.execInContainer("/bin/sh", "-c", "head -c 10 /dhfs_test/fuse/10MB.bin").getExitCode());
-        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container3.execInContainer("/bin/sh", "-c", "rm /dhfs_test/fuse/10MB.bin").getExitCode());
-        await().atMost(45, TimeUnit.SECONDS).until(() -> checkEmpty());
-    }
-
    @Test
    void gccHelloWorldTest() throws IOException, InterruptedException, TimeoutException {
        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container1.execInContainer("/bin/sh", "-c", "echo '#include<stdio.h>\nint main(){printf(\"hello world\"); return 0;}' > /dhfs_test/fuse/hello.c").getExitCode());
@@ -207,21 +175,22 @@ public class DhfsFusex3IT {
    @Test
    void dirConflictTest() throws IOException, InterruptedException, TimeoutException {
        var client = DockerClientFactory.instance().client();
-        client.pauseContainerCmd(container1.getContainerId()).exec();
-        client.pauseContainerCmd(container2.getContainerId()).exec();
-        // Pauses needed as otherwise docker buffers some incoming packets
+
+        client.disconnectFromNetworkCmd().withContainerId(container1.getContainerId()).withNetworkId(network.getId()).exec();
+        client.disconnectFromNetworkCmd().withContainerId(container2.getContainerId()).withNetworkId(network.getId()).exec();
+        client.disconnectFromNetworkCmd().withContainerId(container3.getContainerId()).withNetworkId(network.getId()).exec();
+
        waitingConsumer3.waitUntil(frame -> frame.getUtf8String().contains("Lost connection to"), 60, TimeUnit.SECONDS, 2);
        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container3.execInContainer("/bin/sh", "-c", "echo test3 >> /dhfs_test/fuse/testf").getExitCode());
-        client.pauseContainerCmd(container3.getContainerId()).exec();
-        client.unpauseContainerCmd(container2.getContainerId()).exec();
        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Lost connection to"), 60, TimeUnit.SECONDS, 2);
        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container2.execInContainer("/bin/sh", "-c", "echo test2 >> /dhfs_test/fuse/testf").getExitCode());
-        client.pauseContainerCmd(container2.getContainerId()).exec();
-        client.unpauseContainerCmd(container1.getContainerId()).exec();
        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Lost connection to"), 60, TimeUnit.SECONDS, 2);
        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container1.execInContainer("/bin/sh", "-c", "echo test1 >> /dhfs_test/fuse/testf").getExitCode());
-        client.unpauseContainerCmd(container2.getContainerId()).exec();
-        client.unpauseContainerCmd(container3.getContainerId()).exec();
+
+        client.connectToNetworkCmd().withContainerId(container1.getContainerId()).withNetworkId(network.getId()).exec();
+        client.connectToNetworkCmd().withContainerId(container2.getContainerId()).withNetworkId(network.getId()).exec();
+        client.connectToNetworkCmd().withContainerId(container3.getContainerId()).withNetworkId(network.getId()).exec();
+
        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Connected"), 60, TimeUnit.SECONDS, 2);
        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Connected"), 60, TimeUnit.SECONDS, 2);
        waitingConsumer3.waitUntil(frame -> frame.getUtf8String().contains("Connected"), 60, TimeUnit.SECONDS, 2);
--- a/dhfs-parent/dhfs-fuse/src/test/java/com/usatiuk/dhfsfuse/integration/DhfsImage.java
+++ b/dhfs-parent/dhfs-fuse/src/test/java/com/usatiuk/dhfsfuse/integration/DhfsImage.java
@@ -66,7 +66,7 @@ public class DhfsImage implements Future<String> {
                                .run("apt update && apt install -y libfuse2 curl gcc")
                                .copy("/app", "/app")
                                .copy("/libs", "/libs")
-                                .cmd("java", "-ea", "-Xmx256M", "-XX:TieredStopAtLevel=1", "-XX:+UseParallelGC",
+                                .cmd("java", "-ea", "-Xmx512M", "-XX:+UseParallelGC",
                                        "--add-exports", "java.base/sun.nio.ch=ALL-UNNAMED",
                                        "--add-exports", "java.base/jdk.internal.access=ALL-UNNAMED",
                                        "--add-opens=java.base/java.nio=ALL-UNNAMED",
@@ -87,7 +87,7 @@ public class DhfsImage implements Future<String> {
                                        "-Dquarkus.log.category.\"com.usatiuk.objects.transaction\".level=INFO",
                                        "-Ddhfs.objects.periodic-push-op-interval=5s",
                                        "-Ddhfs.fuse.root=/dhfs_test/fuse",
-                                        "-Ddhfs.objects.persistence.files.root=/dhfs_test/data",
+                                        "-Ddhfs.objects.persistence.root=/dhfs_test/data",
                                        "-Ddhfs.objects.persistence.stuff.root=/dhfs_test/data/stuff",
                                        "-jar", "/app/quarkus-run.jar")
                                .run("mkdir /dhfs_test && chmod 777 /dhfs_test")
--- a/dhfs-parent/dhfs-fuse/src/test/java/com/usatiuk/dhfsfuse/integration/KillIT.java
+++ b/dhfs-parent/dhfs-fuse/src/test/java/com/usatiuk/dhfsfuse/integration/KillIT.java
@@ -52,12 +52,12 @@ public class KillIT {
        container1 = new GenericContainer<>(DhfsImage.getInstance())
                .withPrivilegedMode(true)
                .withCreateContainerCmdModifier(cmd -> Objects.requireNonNull(cmd.getHostConfig()).withDevices(Device.parse("/dev/fuse")))
-                .waitingFor(Wait.forLogMessage(".*Listening.*", 1).withStartupTimeout(Duration.ofSeconds(60))).withNetwork(network)
+                .withNetwork(network)
                .withFileSystemBind(data1.getAbsolutePath(), "/dhfs_test/data");
        container2 = new GenericContainer<>(DhfsImage.getInstance())
                .withPrivilegedMode(true)
                .withCreateContainerCmdModifier(cmd -> Objects.requireNonNull(cmd.getHostConfig()).withDevices(Device.parse("/dev/fuse")))
-                .waitingFor(Wait.forLogMessage(".*Listening.*", 1).withStartupTimeout(Duration.ofSeconds(60))).withNetwork(network)
+                .withNetwork(network)
                .withFileSystemBind(data2.getAbsolutePath(), "/dhfs_test/data");

        Stream.of(container1, container2).parallel().forEach(GenericContainer::start);
@@ -69,8 +69,11 @@ public class KillIT {
        var loggingConsumer2 = new Slf4jLogConsumer(LoggerFactory.getLogger(KillIT.class)).withPrefix("2-" + testInfo.getDisplayName());
        container2.followOutput(loggingConsumer2.andThen(waitingConsumer2));

-        c1uuid = container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
-        c2uuid = container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
+        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Listening"), 60, TimeUnit.SECONDS);
+        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Listening"), 60, TimeUnit.SECONDS);
+
+        c1uuid = container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/self_uuid").getStdout();
+        c2uuid = container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/self_uuid").getStdout();

        Assertions.assertDoesNotThrow(() -> UUID.fromString(c1uuid));
        Assertions.assertDoesNotThrow(() -> UUID.fromString(c2uuid));
--- a/dhfs-parent/dhfs-fuse/src/test/java/com/usatiuk/dhfsfuse/integration/LazyFsIT.java
+++ b/dhfs-parent/dhfs-fuse/src/test/java/com/usatiuk/dhfsfuse/integration/LazyFsIT.java
@@ -12,12 +12,10 @@ import org.testcontainers.containers.GenericContainer;
 import org.testcontainers.containers.Network;
 import org.testcontainers.containers.output.Slf4jLogConsumer;
 import org.testcontainers.containers.output.WaitingConsumer;
-import org.testcontainers.containers.wait.strategy.Wait;

 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Files;
-import java.time.Duration;
 import java.util.Objects;
 import java.util.UUID;
 import java.util.concurrent.*;
@@ -25,6 +23,7 @@ import java.util.stream.Stream;

 import static org.awaitility.Awaitility.await;

+@Disabled
 public class LazyFsIT {
    GenericContainer<?> container1;
    GenericContainer<?> container2;
@@ -64,12 +63,12 @@ public class LazyFsIT {
        container1 = new GenericContainer<>(DhfsImage.getInstance())
                .withPrivilegedMode(true)
                .withCreateContainerCmdModifier(cmd -> Objects.requireNonNull(cmd.getHostConfig()).withDevices(Device.parse("/dev/fuse")))
-                .waitingFor(Wait.forLogMessage(".*Listening.*", 1).withStartupTimeout(Duration.ofSeconds(60))).withNetwork(network)
+                .withNetwork(network)
                .withFileSystemBind(data1.getAbsolutePath(), "/dhfs_test/data");
        container2 = new GenericContainer<>(DhfsImage.getInstance())
                .withPrivilegedMode(true)
                .withCreateContainerCmdModifier(cmd -> Objects.requireNonNull(cmd.getHostConfig()).withDevices(Device.parse("/dev/fuse")))
-                .waitingFor(Wait.forLogMessage(".*Listening.*", 1).withStartupTimeout(Duration.ofSeconds(60))).withNetwork(network)
+                .withNetwork(network)
                .withFileSystemBind(data2.getAbsolutePath(), "/dhfs_test/data");

        Stream.of(container1, container2).parallel().forEach(GenericContainer::start);
@@ -81,8 +80,11 @@ public class LazyFsIT {
        var loggingConsumer2 = new Slf4jLogConsumer(LoggerFactory.getLogger(LazyFsIT.class)).withPrefix("2-" + testInfo.getDisplayName());
        container2.followOutput(loggingConsumer2.andThen(waitingConsumer2));

-        c1uuid = container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
-        c2uuid = container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
+        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Listening"), 60, TimeUnit.SECONDS);
+        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Listening"), 60, TimeUnit.SECONDS);
+
+        c1uuid = container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/self_uuid").getStdout();
+        c2uuid = container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/self_uuid").getStdout();

        Assertions.assertDoesNotThrow(() -> UUID.fromString(c1uuid));
        Assertions.assertDoesNotThrow(() -> UUID.fromString(c2uuid));
@@ -122,7 +124,7 @@ public class LazyFsIT {
    }

    private void checkConsistency(String testName) {
-        await().atMost(45, TimeUnit.SECONDS).until(() -> {
+        await().atMost(120, TimeUnit.SECONDS).until(() -> {
            var ls1 = container1.execInContainer("/bin/sh", "-c", "ls /dhfs_test/fuse");
            var cat1 = container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/fuse/*");
            var ls2 = container2.execInContainer("/bin/sh", "-c", "ls /dhfs_test/fuse");
--- a/dhfs-parent/dhfs-fuse/src/test/java/com/usatiuk/dhfsfuse/integration/ResyncIT.java
+++ b/dhfs-parent/dhfs-fuse/src/test/java/com/usatiuk/dhfsfuse/integration/ResyncIT.java
@@ -38,11 +38,11 @@ public class ResyncIT {
        container1 = new GenericContainer<>(DhfsImage.getInstance())
                .withPrivilegedMode(true)
                .withCreateContainerCmdModifier(cmd -> Objects.requireNonNull(cmd.getHostConfig()).withDevices(Device.parse("/dev/fuse")))
-                .waitingFor(Wait.forLogMessage(".*Listening.*", 1).withStartupTimeout(Duration.ofSeconds(60))).withNetwork(network);
+                .withNetwork(network);
        container2 = new GenericContainer<>(DhfsImage.getInstance())
                .withPrivilegedMode(true)
                .withCreateContainerCmdModifier(cmd -> Objects.requireNonNull(cmd.getHostConfig()).withDevices(Device.parse("/dev/fuse")))
-                .waitingFor(Wait.forLogMessage(".*Listening.*", 1).withStartupTimeout(Duration.ofSeconds(60))).withNetwork(network);
+                .withNetwork(network);

        Stream.of(container1, container2).parallel().forEach(GenericContainer::start);

@@ -52,6 +52,9 @@ public class ResyncIT {
        waitingConsumer2 = new WaitingConsumer();
        var loggingConsumer2 = new Slf4jLogConsumer(LoggerFactory.getLogger(DhfsFuseIT.class)).withPrefix("2-" + testInfo.getDisplayName());
        container2.followOutput(loggingConsumer2.andThen(waitingConsumer2));
+
+        waitingConsumer2.waitUntil(frame -> frame.getUtf8String().contains("Listening"), 60, TimeUnit.SECONDS);
+        waitingConsumer1.waitUntil(frame -> frame.getUtf8String().contains("Listening"), 60, TimeUnit.SECONDS);
    }

    @AfterEach
@@ -63,8 +66,8 @@ public class ResyncIT {
    @Test
    void readWriteFileTest() throws IOException, InterruptedException, TimeoutException {
        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container1.execInContainer("/bin/sh", "-c", "echo tesempty > /dhfs_test/fuse/testf1").getExitCode());
-        c1uuid = container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
-        c2uuid = container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
+        c1uuid = container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/self_uuid").getStdout();
+        c2uuid = container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/self_uuid").getStdout();

        Assertions.assertDoesNotThrow(() -> UUID.fromString(c1uuid));
        Assertions.assertDoesNotThrow(() -> UUID.fromString(c2uuid));
@@ -103,8 +106,8 @@ public class ResyncIT {
        foundWc = container2.execInContainer("/bin/sh", "-c", "find /dhfs_test/fuse -type f | wc -l");
        Assertions.assertEquals(200, Integer.valueOf(foundWc.getStdout().strip()));

-        c1uuid = container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
-        c2uuid = container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
+        c1uuid = container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/self_uuid").getStdout();
+        c2uuid = container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/self_uuid").getStdout();

        Assertions.assertDoesNotThrow(() -> UUID.fromString(c1uuid));
        Assertions.assertDoesNotThrow(() -> UUID.fromString(c2uuid));
@@ -143,8 +146,8 @@ public class ResyncIT {
        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container1.execInContainer("/bin/sh", "-c", "mv /dhfs_test/fuse/testd1 /dhfs_test/fuse/testd2").getExitCode());
        await().atMost(45, TimeUnit.SECONDS).until(() -> 0 == container1.execInContainer("/bin/sh", "-c", "echo tesempty2 > /dhfs_test/fuse/testd2/testf2").getExitCode());

-        c1uuid = container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
-        c2uuid = container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/stuff/self_uuid").getStdout();
+        c1uuid = container1.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/self_uuid").getStdout();
+        c2uuid = container2.execInContainer("/bin/sh", "-c", "cat /dhfs_test/data/self_uuid").getStdout();

        Assertions.assertDoesNotThrow(() -> UUID.fromString(c1uuid));
        Assertions.assertDoesNotThrow(() -> UUID.fromString(c2uuid));
--- a/dhfs-parent/dhfs-fuse/src/test/resources/application.properties
+++ b/dhfs-parent/dhfs-fuse/src/test/resources/application.properties
@@ -1,5 +1,4 @@
-dhfs.objects.persistence.files.root=${HOME}/dhfs_data/dhfs_root_test
-dhfs.objects.root=${HOME}/dhfs_data/dhfs_root_d_test
+dhfs.objects.persistence.root=${HOME}/dhfs_data/dhfs_root_test
 dhfs.fuse.root=${HOME}/dhfs_data/dhfs_fuse_root_test
 dhfs.objects.ref_verification=true
 dhfs.objects.deletion.delay=0
--- a/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/AlreadyExistsException.java
+++ b/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/AlreadyExistsException.java
@@ -1,5 +1,8 @@
 package com.usatiuk.kleppmanntree;

+/**
+ * Exception thrown when an attempt is made to create a new tree node as a child with a name that already exists.
+ */
 public class AlreadyExistsException extends RuntimeException {
    public AlreadyExistsException(String message) {
        super(message);
--- a/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/AtomicClock.java
+++ b/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/AtomicClock.java
@@ -1,32 +0,0 @@
-package com.usatiuk.kleppmanntree;
-
-import java.io.Serializable;
-
-public class AtomicClock implements Clock<Long>, Serializable {
-    private long _max = 0;
-
-    public AtomicClock(long counter) {
-        _max = counter;
-    }
-
-    @Override
-    public Long getTimestamp() {
-        return ++_max;
-    }
-
-    public void setTimestamp(Long timestamp) {
-        _max = timestamp;
-    }
-
-    @Override
-    public Long peekTimestamp() {
-        return _max;
-    }
-
-    @Override
-    public Long updateTimestamp(Long receivedTimestamp) {
-        var old = _max;
-        _max = Math.max(_max, receivedTimestamp) + 1;
-        return old;
-    }
-}
--- a/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/Clock.java
+++ b/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/Clock.java
@@ -1,9 +1,26 @@
 package com.usatiuk.kleppmanntree;

+/**
+ * Clock interface
+ */
 public interface Clock<TimestampT extends Comparable<TimestampT>> {
+    /**
+     * Increment and get the current timestamp.
+     * @return the incremented timestamp
+     */
    TimestampT getTimestamp();

+    /**
+     * Get the current timestamp without incrementing it.
+     * @return the current timestamp
+     */
    TimestampT peekTimestamp();

+    /**
+     * Update the timestamp with an externally received timestamp.
+     * Will set the currently stored timestamp to <code>max(receivedTimestamp, currentTimestamp) + 1</code>
+     * @param receivedTimestamp the received timestamp
+     * @return the previous timestamp
+     */
    TimestampT updateTimestamp(TimestampT receivedTimestamp);
 }
--- a/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/CombinedTimestamp.java
+++ b/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/CombinedTimestamp.java
@@ -3,6 +3,13 @@ package com.usatiuk.kleppmanntree;
 import java.io.Serializable;
 import java.util.Comparator;

+/**
+ * CombinedTimestamp is a record that represents a timestamp and a node ID, ordered first by timestamp and then by node ID.
+ * @param timestamp the timestamp
+ * @param nodeId the node ID. If null, then only the timestamp is used for ordering.
+ * @param <TimestampT> the type of the timestamp
+ * @param <PeerIdT> the type of the node ID
+ */
 public record CombinedTimestamp<TimestampT extends Comparable<TimestampT>, PeerIdT extends Comparable<PeerIdT>>
        (TimestampT timestamp,
         PeerIdT nodeId) implements Comparable<CombinedTimestamp<TimestampT, PeerIdT>>, Serializable {
--- a/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/KleppmannTree.java
+++ b/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/KleppmannTree.java
@@ -8,6 +8,14 @@ import java.util.function.Function;
 import java.util.logging.Level;
 import java.util.logging.Logger;

+/**
+ * An implementation of a tree as described in <a href="https://martin.kleppmann.com/papers/move-op.pdf">A highly-available move operation for replicated trees</a>
+ *
+ * @param <TimestampT> Type of the timestamp
+ * @param <PeerIdT>    Type of the peer ID
+ * @param <MetaT>      Type of the node metadata
+ * @param <NodeIdT>    Type of the node ID
+ */
 public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT extends Comparable<PeerIdT>, MetaT extends NodeMeta, NodeIdT> {
    private static final Logger LOGGER = Logger.getLogger(KleppmannTree.class.getName());

@@ -16,6 +24,14 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
    private final Clock<TimestampT> _clock;
    private final OpRecorder<TimestampT, PeerIdT, MetaT, NodeIdT> _opRecorder;

+    /**
+     * Constructor with all the dependencies
+     *
+     * @param storage    Storage interface
+     * @param peers      Peer interface
+     * @param clock      Clock interface
+     * @param opRecorder Operation recorder interface
+     */
    public KleppmannTree(StorageInterface<TimestampT, PeerIdT, MetaT, NodeIdT> storage,
                         PeerInterface<PeerIdT> peers,
                         Clock<TimestampT> clock,
@@ -26,6 +42,13 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
        _opRecorder = opRecorder;
    }

+    /**
+     * Traverse the tree from the given node ID using the given list of names
+     *
+     * @param fromId The starting node ID
+     * @param names  The list of names to traverse
+     * @return The resulting node ID or null if not found
+     */
    private NodeIdT traverseImpl(NodeIdT fromId, List<String> names) {
        if (names.isEmpty()) return fromId;

@@ -39,14 +62,21 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
        return traverseImpl(childId, names.subList(1, names.size()));
    }

-    public NodeIdT traverse(NodeIdT fromId, List<String> names) {
-        return traverseImpl(fromId, names.subList(1, names.size()));
-    }
-
+    /**
+     * Traverse the tree from its root node using the given list of names
+     *
+     * @param names The list of names to traverse
+     * @return The resulting node ID or null if not found
+     */
    public NodeIdT traverse(List<String> names) {
        return traverseImpl(_storage.getRootId(), names);
    }

+    /**
+     * Undo the effect of a log effect
+     *
+     * @param effect The log effect to undo
+     */
    private void undoEffect(LogEffect<TimestampT, PeerIdT, MetaT, NodeIdT> effect) {
        if (effect.oldInfo() != null) {
            var node = _storage.getById(effect.childId());
@@ -89,6 +119,11 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
        }
    }

+    /**
+     * Undo the effects of a log record
+     *
+     * @param op The log record to undo
+     */
    private void undoOp(LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT> op) {
        LOGGER.finer(() -> "Will undo op: " + op);
        if (op.effects() != null)
@@ -96,16 +131,32 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
                undoEffect(e);
    }

+    /**
+     * Redo the operation in a log record
+     *
+     * @param entry The log record to redo
+     */
    private void redoOp(Map.Entry<CombinedTimestamp<TimestampT, PeerIdT>, LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT>> entry) {
        var newEffects = doOp(entry.getValue().op(), false);
        _storage.getLog().replace(entry.getKey(), newEffects);
    }

+    /**
+     * Perform the operation and put it in the log
+     *
+     * @param op                   The operation to perform
+     * @param failCreatingIfExists Whether to fail if there is a name conflict,
+     *                             otherwise replace the existing node
+     * @throws AlreadyExistsException If the node already exists and failCreatingIfExists is true
+     */
    private void doAndPut(OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> op, boolean failCreatingIfExists) {
        var res = doOp(op, failCreatingIfExists);
        _storage.getLog().put(res.op().timestamp(), res);
    }

+    /**
+     * Try to trim the log to the causality threshold
+     */
    private void tryTrimLog() {
        var log = _storage.getLog();
        var timeLog = _storage.getPeerTimestampLog();
@@ -161,22 +212,52 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
        }
    }

+    /**
+     * Move a node to a new parent with new metadata
+     *
+     * @param newParent The new parent node ID
+     * @param newMeta   The new metadata
+     * @param child     The child node ID
+     * @throws AlreadyExistsException If the node already exists and failCreatingIfExists is true
+     */
    public <LocalMetaT extends MetaT> void move(NodeIdT newParent, LocalMetaT newMeta, NodeIdT child) {
        move(newParent, newMeta, child, true);
    }

+    /**
+     * Move a node to a new parent with new metadata
+     *
+     * @param newParent            The new parent node ID
+     * @param newMeta              The new metadata
+     * @param child                The child node ID
+     * @param failCreatingIfExists Whether to fail if there is a name conflict,
+     *                             otherwise replace the existing node
+     * @throws AlreadyExistsException If the node already exists and failCreatingIfExists is true
+     */
    public void move(NodeIdT newParent, MetaT newMeta, NodeIdT child, boolean failCreatingIfExists) {
        var createdMove = createMove(newParent, newMeta, child);
        applyOp(_peers.getSelfId(), createdMove, failCreatingIfExists);
        _opRecorder.recordOp(createdMove);
    }

+    /**
+     * Apply an external operation from a remote peer
+     *
+     * @param from The peer ID
+     * @param op   The operation to apply
+     */
    public void applyExternalOp(PeerIdT from, OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> op) {
        _clock.updateTimestamp(op.timestamp().timestamp());
        applyOp(from, op, false);
    }

-    // Returns true if the timestamp is newer than what's seen, false otherwise
+    /**
+     * Update the causality threshold timestamp for a peer
+     *
+     * @param from         The peer ID
+     * @param newTimestamp The timestamp received from it
+     * @return True if the timestamp was updated, false otherwise
+     */
    private boolean updateTimestampImpl(PeerIdT from, TimestampT newTimestamp) {
        TimestampT oldRef = _storage.getPeerTimestampLog().getForPeer(from);
        if (oldRef != null && oldRef.compareTo(newTimestamp) >= 0) { // FIXME?
@@ -187,6 +268,12 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
        return true;
    }

+    /**
+     * Update the causality threshold timestamp for a peer
+     *
+     * @param from      The peer ID
+     * @param timestamp The timestamp received from it
+     */
    public void updateExternalTimestamp(PeerIdT from, TimestampT timestamp) {
        var gotExt = _storage.getPeerTimestampLog().getForPeer(from);
        var gotSelf = _storage.getPeerTimestampLog().getForPeer(_peers.getSelfId());
@@ -197,6 +284,15 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
        tryTrimLog();
    }

+    /**
+     * Apply an operation from a peer
+     *
+     * @param from                 The peer ID
+     * @param op                   The operation to apply
+     * @param failCreatingIfExists Whether to fail if there is a name conflict,
+     *                             otherwise replace the existing node
+     * @throws AlreadyExistsException If the node already exists and failCreatingIfExists is true
+     */
    private void applyOp(PeerIdT from, OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> op, boolean failCreatingIfExists) {
        if (!updateTimestampImpl(op.timestamp().nodeId(), op.timestamp().timestamp())) return;

@@ -229,14 +325,36 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
        }
    }

+    /**
+     * Get a new timestamp, incrementing the one in storage
+     *
+     * @return A new timestamp
+     */
    private CombinedTimestamp<TimestampT, PeerIdT> getTimestamp() {
        return new CombinedTimestamp<>(_clock.getTimestamp(), _peers.getSelfId());
    }

+    /**
+     * Create a new move operation
+     *
+     * @param newParent The new parent node ID
+     * @param newMeta   The new metadata
+     * @param node      The child node ID
+     * @return A new move operation
+     */
    private <LocalMetaT extends MetaT> OpMove<TimestampT, PeerIdT, LocalMetaT, NodeIdT> createMove(NodeIdT newParent, LocalMetaT newMeta, NodeIdT node) {
        return new OpMove<>(getTimestamp(), newParent, newMeta, node);
    }

+    /**
+     * Perform the operation and return the log record
+     *
+     * @param op                   The operation to perform
+     * @param failCreatingIfExists Whether to fail if there is a name conflict,
+     *                             otherwise replace the existing node
+     * @return The log record
+     * @throws AlreadyExistsException If the node already exists and failCreatingIfExists is true
+     */
    private LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT> doOp(OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> op, boolean failCreatingIfExists) {
        LOGGER.finer(() -> "Doing op: " + op);
        LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT> computed;
@@ -253,10 +371,24 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
        return computed;
    }

+    /**
+     * Get a new node from storage
+     *
+     * @param key    The node ID
+     * @param parent The parent node ID
+     * @param meta   The metadata
+     * @return A new tree node
+     */
    private TreeNode<TimestampT, PeerIdT, MetaT, NodeIdT> getNewNode(NodeIdT key, NodeIdT parent, MetaT meta) {
        return _storage.createNewNode(key, parent, meta);
    }

+    /**
+     * Apply the effects of a log record
+     *
+     * @param sourceOp The source operation
+     * @param effects  The list of log effects
+     */
    private void applyEffects(OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> sourceOp, List<LogEffect<TimestampT, PeerIdT, MetaT, NodeIdT>> effects) {
        for (var effect : effects) {
            LOGGER.finer(() -> "Applying effect: " + effect + " from op " + sourceOp);
@@ -297,6 +429,15 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
        }
    }

+    /**
+     * Compute the effects of a move operation
+     *
+     * @param op                   The operation to process
+     * @param failCreatingIfExists Whether to fail if there is a name conflict,
+     *                             otherwise replace the existing node
+     * @return The log record with the computed effects
+     * @throws AlreadyExistsException If the node already exists and failCreatingIfExists is true
+     */
    private LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT> computeEffects(OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> op, boolean failCreatingIfExists) {
        var node = _storage.getById(op.childId());

@@ -380,6 +521,13 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
        ));
    }

+    /**
+     * Check if a node is an ancestor of another node
+     *
+     * @param child  The child node ID
+     * @param parent The parent node ID
+     * @return True if the child is an ancestor of the parent, false otherwise
+     */
    private boolean isAncestor(NodeIdT child, NodeIdT parent) {
        var node = _storage.getById(parent);
        NodeIdT curParent;
@@ -390,6 +538,11 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
        return false;
    }

+    /**
+     * Walk the tree and apply the given consumer to each node
+     *
+     * @param consumer The consumer to apply to each node
+     */
    public void walkTree(Consumer<TreeNode<TimestampT, PeerIdT, MetaT, NodeIdT>> consumer) {
        ArrayDeque<NodeIdT> queue = new ArrayDeque<>();
        queue.push(_storage.getRootId());
@@ -403,6 +556,12 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
        }
    }

+    /**
+     * Find the parent of a node that matches the given predicate
+     *
+     * @param kidPredicate The predicate to match the child node
+     * @return A pair containing the name of the child and the ID of the parent, or null if not found
+     */
    public Pair<String, NodeIdT> findParent(Function<TreeNode<TimestampT, PeerIdT, MetaT, NodeIdT>, Boolean> kidPredicate) {
        ArrayDeque<NodeIdT> queue = new ArrayDeque<>();
        queue.push(_storage.getRootId());
@@ -423,6 +582,13 @@ public class KleppmannTree<TimestampT extends Comparable<TimestampT>, PeerIdT ex
        return null;
    }

+    /**
+     * Record the bootstrap operations for a given peer
+     * Will visit all nodes of the tree and add their effective operations to both the queue to be sent to the peer,
+     * and to the global operation log.
+     *
+     * @param host The peer ID
+     */
    public void recordBoostrapFor(PeerIdT host) {
        TreeMap<CombinedTimestamp<TimestampT, PeerIdT>, OpMove<TimestampT, PeerIdT, MetaT, NodeIdT>> result = new TreeMap<>();

--- a/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/LogEffect.java
+++ b/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/LogEffect.java
@@ -2,6 +2,18 @@ package com.usatiuk.kleppmanntree;

 import java.io.Serializable;

+/**
+ * LogEffect is a record that represents the effect of a log entry on a tree node.
+ * @param oldInfo the old information about the node, before it was moved. Null if the node did not exist before
+ * @param effectiveOp the operation that had caused this effect to be applied
+ * @param newParentId the ID of the new parent node
+ * @param newMeta the new metadata of the node
+ * @param childId the ID of the child node
+ * @param <TimestampT> the type of the timestamp
+ * @param <PeerIdT> the type of the peer ID
+ * @param <MetaT> the type of the node metadata
+ * @param <NodeIdT> the type of the node ID
+ */
 public record LogEffect<TimestampT extends Comparable<TimestampT>, PeerIdT extends Comparable<PeerIdT>, MetaT extends NodeMeta, NodeIdT>(
        LogEffectOld<TimestampT, PeerIdT, MetaT, NodeIdT> oldInfo,
        OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> effectiveOp,
--- a/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/LogEffectOld.java
+++ b/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/LogEffectOld.java
@@ -2,6 +2,16 @@ package com.usatiuk.kleppmanntree;

 import java.io.Serializable;

+/**
+ * Represents the old information about a node before it was moved.
+ * @param oldEffectiveMove the old effective move that had caused this effect to be applied
+ * @param oldParent the ID of the old parent node
+ * @param oldMeta the old metadata of the node
+ * @param <TimestampT> the type of the timestamp
+ * @param <PeerIdT> the type of the peer ID
+ * @param <MetaT> the type of the node metadata
+ * @param <NodeIdT> the type of the node ID
+ */
 public record LogEffectOld<TimestampT extends Comparable<TimestampT>, PeerIdT extends Comparable<PeerIdT>, MetaT extends NodeMeta, NodeIdT>
        (OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> oldEffectiveMove,
         NodeIdT oldParent,
--- a/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/LogInterface.java
+++ b/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/LogInterface.java
@@ -4,29 +4,82 @@ import org.apache.commons.lang3.tuple.Pair;

 import java.util.List;

+/**
+ * LogInterface is an interface that allows accessing the log of operations
+ * @param <TimestampT> the type of the timestamp
+ * @param <PeerIdT> the type of the peer ID
+ * @param <MetaT> the type of the node metadata
+ * @param <NodeIdT> the type of the node ID
+ */
 public interface LogInterface<
        TimestampT extends Comparable<TimestampT>,
        PeerIdT extends Comparable<PeerIdT>,
        MetaT extends NodeMeta,
        NodeIdT> {
+    /**
+     * Peek the oldest log entry.
+     * @return the oldest log entry
+     */
    Pair<CombinedTimestamp<TimestampT, PeerIdT>, LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT>> peekOldest();

+    /**
+     * Take the oldest log entry.
+     * @return the oldest log entry
+     */
    Pair<CombinedTimestamp<TimestampT, PeerIdT>, LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT>> takeOldest();

+    /**
+     * Peek the newest log entry.
+     * @return the newest log entry
+     */
    Pair<CombinedTimestamp<TimestampT, PeerIdT>, LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT>> peekNewest();

+    /**
+     * Return all log entries that are newer than the given timestamp.
+     * @param since the timestamp to compare with
+     * @param inclusive if true, include the log entry with the given timestamp
+     * @return a list of log entries that are newer than the given timestamp
+     */
    List<Pair<CombinedTimestamp<TimestampT, PeerIdT>, LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT>>>
    newestSlice(CombinedTimestamp<TimestampT, PeerIdT> since, boolean inclusive);

+    /**
+     * Return all the log entries
+     * @return a list of all log entries
+     */
    List<Pair<CombinedTimestamp<TimestampT, PeerIdT>, LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT>>> getAll();

+    /**
+     * Checks if the log is empty.
+     * @return true if the log is empty, false otherwise
+     */
    boolean isEmpty();

+    /**
+     * Checks if the log contains the given timestamp.
+     * @param timestamp the timestamp to check
+     * @return true if the log contains the given timestamp, false otherwise
+     */
    boolean containsKey(CombinedTimestamp<TimestampT, PeerIdT> timestamp);

+    /**
+     * Get the size of the log.
+     * @return the size of the log (number of entries)
+     */
    long size();

+    /**
+     * Add a log entry to the log.
+     * @param timestamp the timestamp of the log entry
+     * @param record the log entry
+     * @throws IllegalStateException if the log entry already exists
+     */
    void put(CombinedTimestamp<TimestampT, PeerIdT> timestamp, LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT> record);

+    /**
+     * Replace a log entry in the log.
+     * @param timestamp the timestamp of the log entry
+     * @param record the log entry
+     */
    void replace(CombinedTimestamp<TimestampT, PeerIdT> timestamp, LogRecord<TimestampT, PeerIdT, MetaT, NodeIdT> record);
 }
--- a/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/LogRecord.java
+++ b/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/LogRecord.java
@@ -3,6 +3,15 @@ package com.usatiuk.kleppmanntree;
 import java.io.Serializable;
 import java.util.List;

+/**
+ * Represents a log record in the Kleppmann tree.
+ * @param op the operation that is stored in this log record
+ * @param effects the effects of the operation (resulting moves)
+ * @param <TimestampT> the type of the timestamp
+ * @param <PeerIdT> the type of the peer ID
+ * @param <MetaT> the type of the node metadata
+ * @param <NodeIdT> the type of the node ID
+ */
 public record LogRecord<TimestampT extends Comparable<TimestampT>, PeerIdT extends Comparable<PeerIdT>, MetaT extends NodeMeta, NodeIdT>
        (OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> op,
         List<LogEffect<TimestampT, PeerIdT, MetaT, NodeIdT>> effects) implements Serializable {
--- a/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/NodeMeta.java
+++ b/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/NodeMeta.java
@@ -2,8 +2,24 @@ package com.usatiuk.kleppmanntree;

 import java.io.Serializable;

+/**
+ * Represents metadata associated with a node in the Kleppmann tree.
+ * This interface is used to define the metadata that can be associated with nodes in the tree.
+ * Implementations of this interface should provide a name for the node and a method to create a copy of it with a new name.
+ */
 public interface NodeMeta extends Serializable {
+    /**
+     * Returns the name of the node.
+     *
+     * @return the name of the node
+     */
    String name();

+    /**
+     * Creates a copy of the metadata with a new name.
+     *
+     * @param name the new name for the metadata
+     * @return a new instance of NodeMeta with the specified name
+     */
    NodeMeta withName(String name);
 }
--- a/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/OpMove.java
+++ b/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/OpMove.java
@@ -2,9 +2,27 @@ package com.usatiuk.kleppmanntree;

 import java.io.Serializable;

+/**
+ * Operation that moves a child node to a new parent node.
+ *
+ * @param timestamp    the timestamp of the operation
+ * @param newParentId  the ID of the new parent node
+ * @param newMeta      the new metadata of the node, can be null
+ * @param childId      the ID of the child node (the node that is being moved)
+ * @param <TimestampT> the type of the timestamp
+ * @param <PeerIdT>    the type of the peer ID
+ * @param <MetaT>      the type of the node metadata
+ * @param <NodeIdT>    the type of the node ID
+ */
 public record OpMove<TimestampT extends Comparable<TimestampT>, PeerIdT extends Comparable<PeerIdT>, MetaT extends NodeMeta, NodeIdT>
        (CombinedTimestamp<TimestampT, PeerIdT> timestamp, NodeIdT newParentId, MetaT newMeta,
         NodeIdT childId) implements Serializable {
+    /**
+     * Returns the new name of the node: name extracted from the new metadata if available,
+     * otherwise the child ID converted to string.
+     *
+     * @return the new name of the node
+     */
    public String newName() {
        if (newMeta != null)
            return newMeta.name();
--- a/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/OpRecorder.java
+++ b/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/OpRecorder.java
@@ -1,7 +1,26 @@
 package com.usatiuk.kleppmanntree;

+/**
+ * Interface to provide recording operations to be sent to peers asynchronously.
+ * @param <TimestampT> the type of the timestamp
+ * @param <PeerIdT> the type of the peer ID
+ * @param <MetaT> the type of the node metadata
+ * @param <NodeIdT> the type of the node ID
+ */
 public interface OpRecorder<TimestampT extends Comparable<TimestampT>, PeerIdT extends Comparable<PeerIdT>, MetaT extends NodeMeta, NodeIdT> {
+    /**
+     * Records an operation to be sent to peers asynchronously.
+     * The operation will be sent to all known peers in the system.
+     *
+     * @param op the operation to be recorded
+     */
    void recordOp(OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> op);

+    /**
+     * Records an operation to be sent to a specific peer asynchronously.
+     *
+     * @param peer the ID of the peer to send the operation to
+     * @param op   the operation to be recorded
+     */
    void recordOpForPeer(PeerIdT peer, OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> op);
 }
--- a/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/PeerInterface.java
+++ b/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/PeerInterface.java
@@ -2,8 +2,22 @@ package com.usatiuk.kleppmanntree;

 import java.util.Collection;

+/**
+ * Interface providing access to a list of known peers.
+ * @param <PeerIdT> the type of the peer ID
+ */
 public interface PeerInterface<PeerIdT extends Comparable<PeerIdT>> {
+    /**
+     * Returns the ID of the current peer.
+     *
+     * @return the ID of the current peer
+     */
    PeerIdT getSelfId();

+    /**
+     * Returns a collection of all known peers.
+     *
+     * @return a collection of all known peers
+     */
    Collection<PeerIdT> getAllPeers();
 }
--- a/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/PeerTimestampLogInterface.java
+++ b/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/PeerTimestampLogInterface.java
@@ -1,11 +1,26 @@
 package com.usatiuk.kleppmanntree;

+/**
+ * Interface providing a map of newest received timestamps for each peer. (causality thresholds)
+ * If a peer has some timestamp recorded in this map,
+ * it means that all messages coming from this peer will have a newer timestamp.
+ * @param <TimestampT>
+ * @param <PeerIdT>
+ */
 public interface PeerTimestampLogInterface<
        TimestampT extends Comparable<TimestampT>,
        PeerIdT extends Comparable<PeerIdT>> {

+    /**
+     * Get the timestamp for a specific peer.
+     * @param peerId the ID of the peer
+     * @return the timestamp for the peer
+     */
    TimestampT getForPeer(PeerIdT peerId);

+    /**
+     * Get the timestamp for the current peer.
+     */
    void putForPeer(PeerIdT peerId, TimestampT timestamp);

 }
--- a/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/StorageInterface.java
+++ b/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/StorageInterface.java
@@ -1,28 +1,89 @@
 package com.usatiuk.kleppmanntree;

+/**
+ * Storage interface for the Kleppmann tree.
+ *
+ * @param <TimestampT> the type of the timestamp
+ * @param <PeerIdT>    the type of the peer ID
+ * @param <MetaT>      the type of the node metadata
+ * @param <NodeIdT>    the type of the node ID
+ */
 public interface StorageInterface<
        TimestampT extends Comparable<TimestampT>,
        PeerIdT extends Comparable<PeerIdT>,
        MetaT extends NodeMeta,
        NodeIdT> {
+    /**
+     * Get the root node ID.
+     *
+     * @return the root node IDx
+     */
    NodeIdT getRootId();

+    /**
+     * Get the trash node ID.
+     *
+     * @return the trash node ID
+     */
    NodeIdT getTrashId();

+    /**
+     * Get the lost and found node ID.
+     *
+     * @return the lost and found node ID
+     */
    NodeIdT getLostFoundId();

+    /**
+     * Get the new node ID.
+     *
+     * @return the new node ID
+     */
    NodeIdT getNewNodeId();

+    /**
+     * Get the node by its ID.
+     *
+     * @param id the ID of the node
+     * @return the node with the specified ID, or null if not found
+     */
    TreeNode<TimestampT, PeerIdT, MetaT, NodeIdT> getById(NodeIdT id);

-    // Creates a node, returned wrapper is RW-locked
+    /**
+     * Create a new node with the specified key, parent, and metadata.
+     *
+     * @param key    the ID of the new node
+     * @param parent the ID of the parent node
+     * @param meta   the metadata of the new node
+     * @return the new node
+     */
    TreeNode<TimestampT, PeerIdT, MetaT, NodeIdT> createNewNode(NodeIdT key, NodeIdT parent, MetaT meta);

+    /**
+     * Put a node into the storage.
+     *
+     * @param node the node to put into the storage
+     */
    void putNode(TreeNode<TimestampT, PeerIdT, MetaT, NodeIdT> node);

+    /**
+     * Remove a node from the storage.
+     *
+     * @param id the ID of the node to remove
+     */
    void removeNode(NodeIdT id);

+    /**
+     * Get the log interface.
+     *
+     * @return the log interface
+     */
    LogInterface<TimestampT, PeerIdT, MetaT, NodeIdT> getLog();

+    /**
+     * Get the peer timestamp log interface.
+     *
+     * @return the peer timestamp log interface
+     */
    PeerTimestampLogInterface<TimestampT, PeerIdT> getPeerTimestampLog();
 }
--- a/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/TreeNode.java
+++ b/dhfs-parent/kleppmanntree/src/main/java/com/usatiuk/kleppmanntree/TreeNode.java
@@ -5,29 +5,92 @@ import org.pcollections.PMap;

 import java.io.Serializable;

+/**
+ * Represents a node in the Kleppmann tree.
+ *
+ * @param <TimestampT> the type of the timestamp
+ * @param <PeerIdT>    the type of the peer ID
+ * @param <MetaT>      the type of the node metadata
+ * @param <NodeIdT>    the type of the node ID
+ */
 public interface TreeNode<TimestampT extends Comparable<TimestampT>, PeerIdT extends Comparable<PeerIdT>, MetaT extends NodeMeta, NodeIdT> extends Serializable {
+    /**
+     * Get the ID of the node.
+     *
+     * @return the ID of the node
+     */
    NodeIdT key();

+    /**
+     * Get the ID of the parent node.
+     *
+     * @return the ID of the parent node
+     */
    NodeIdT parent();

+    /**
+     * Get the last effective operation that moved this node.
+     *
+     * @return the last effective operation
+     */
    OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> lastEffectiveOp();

+    /**
+     * Get the metadata stored in this node.
+     *
+     * @return the metadata of the node
+     */
    @Nullable
    MetaT meta();

+    /**
+     * Get the name of the node.
+     * If the node has metadata, the name is extracted from it, otherwise the key is converted to string.
+     *
+     * @return the name of the node
+     */
    default String name() {
        var meta = meta();
        if (meta != null) return meta.name();
        return key().toString();
    }

+    /**
+     * Get the children of this node.
+     *
+     * @return a map of child IDs to their respective nodes
+     */
    PMap<String, NodeIdT> children();

+    /**
+     * Make a copy of this node with a new parent.
+     *
+     * @param parent the ID of the new parent node
+     * @return a new TreeNode instance with the updated parent
+     */
    TreeNode<TimestampT, PeerIdT, MetaT, NodeIdT> withParent(NodeIdT parent);

+    /**
+     * Make a copy of this node with a new last effective operation.
+     *
+     * @param lastEffectiveOp the new last effective operation
+     * @return a new TreeNode instance with the updated last effective operation
+     */
    TreeNode<TimestampT, PeerIdT, MetaT, NodeIdT> withLastEffectiveOp(OpMove<TimestampT, PeerIdT, MetaT, NodeIdT> lastEffectiveOp);

+    /**
+     * Make a copy of this node with new metadata.
+     *
+     * @param meta the new metadata
+     * @return a new TreeNode instance with the updated metadata
+     */
    TreeNode<TimestampT, PeerIdT, MetaT, NodeIdT> withMeta(MetaT meta);

+    /**
+     * Make a copy of this node with new children.
+     *
+     * @param children the new children
+     * @return a new TreeNode instance with the updated children
+     */
    TreeNode<TimestampT, PeerIdT, MetaT, NodeIdT> withChildren(PMap<String, NodeIdT> children);
 }
--- a/dhfs-parent/objects/pom.xml
+++ b/dhfs-parent/objects/pom.xml
@@ -18,6 +18,11 @@
    </properties>

    <dependencies>
+        <dependency>
+            <groupId>com.github.ben-manes.caffeine</groupId>
+            <artifactId>caffeine</artifactId>
+            <version>3.2.2</version>
+        </dependency>
        <dependency>
            <groupId>net.jqwik</groupId>
            <artifactId>jqwik</artifactId>
@@ -36,10 +41,6 @@
            <groupId>io.quarkus</groupId>
            <artifactId>quarkus-grpc</artifactId>
        </dependency>
-        <dependency>
-            <groupId>net.openhft</groupId>
-            <artifactId>zero-allocation-hashing</artifactId>
-        </dependency>
        <dependency>
            <groupId>org.junit.jupiter</groupId>
            <artifactId>junit-jupiter-engine</artifactId>
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/JData.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/JData.java
@@ -2,9 +2,20 @@ package com.usatiuk.objects;

 import java.io.Serializable;

+/**
+ * JData is a marker interface for all objects that can be stored in the object store.
+ */
 public interface JData extends Serializable {
+    /**
+     * Returns the key of the object.
+     * @return the key of the object
+     */
    JObjectKey key();

+    /**
+     * Returns the estimated size of the object in bytes.
+     * @return the estimated size of the object in bytes
+     */
    default int estimateSize() {
        return 100;
    }
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/JDataVersionedWrapper.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/JDataVersionedWrapper.java
@@ -2,15 +2,34 @@ package com.usatiuk.objects;

 import com.usatiuk.objects.iterators.Data;

+/**
+ * JDataVersionedWrapper is a wrapper for JData that contains its version number
+ * (the id of the transaction that had changed it last)
+ */
 public sealed interface JDataVersionedWrapper extends Data<JDataVersionedWrapper> permits JDataVersionedWrapperLazy, JDataVersionedWrapperImpl {
    @Override
    default JDataVersionedWrapper value() {
        return this;
    }

+    /**
+     * Returns the wrapped object.
+     *
+     * @return the wrapped object
+     */
    JData data();

+    /**
+     * Returns the version number of the object.
+     *
+     * @return the version number of the object
+     */
    long version();

+    /**
+     * Returns the estimated size of the object in bytes.
+     *
+     * @return the estimated size of the object in bytes
+     */
    int estimateSize();
 }
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/JDataVersionedWrapperImpl.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/JDataVersionedWrapperImpl.java
@@ -4,6 +4,9 @@ import jakarta.annotation.Nonnull;

 import java.io.Serializable;

+/**
+ * Simple wrapper for an already-existing JData object with a version.
+ */
 public record JDataVersionedWrapperImpl(@Nonnull JData data,
                                        long version) implements Serializable, JDataVersionedWrapper {
    @Override
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/JDataVersionedWrapperLazy.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/JDataVersionedWrapperLazy.java
@@ -2,18 +2,35 @@ package com.usatiuk.objects;

 import java.util.function.Supplier;

+/**
+ * Lazy JDataVersionedWrapper implementation.
+ * The object is deserialized only when data() is called for the first time.
+ * Also allows to set a callback to be called when the data is loaded (e.g. to cache it).
+ */
 public final class JDataVersionedWrapperLazy implements JDataVersionedWrapper {
    private final long _version;
    private final int _estimatedSize;
    private JData _data;
    private Supplier<JData> _producer;

+    /**
+     * Creates a new JDataVersionedWrapperLazy object.
+     *
+     * @param version       the version number of the object
+     * @param estimatedSize the estimated size of the object in bytes
+     * @param producer      a supplier that produces the wrapped object
+     */
    public JDataVersionedWrapperLazy(long version, int estimatedSize, Supplier<JData> producer) {
        _version = version;
        _estimatedSize = estimatedSize;
        _producer = producer;
    }

+    /**
+     * Set a callback to be called when the data is loaded.
+     *
+     * @param cacheCallback the callback to be called
+     */
    public void setCacheCallback(Runnable cacheCallback) {
        if (_data != null) {
            throw new IllegalStateException("Cache callback can be set only before data is loaded");
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/JDataVersionedWrapperSerializer.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/JDataVersionedWrapperSerializer.java
@@ -7,11 +7,21 @@ import jakarta.inject.Singleton;

 import java.nio.ByteBuffer;

+/**
+ * Serializer for JDataVersionedWrapper objects.
+ * The objects are stored in a simple format: first is 8-byte long, then the serialized object.
+ */
@Singleton
 public class JDataVersionedWrapperSerializer {
    @Inject
    ObjectSerializer<JData> dataSerializer;

+    /**
+     * Serializes a JDataVersionedWrapper object to a ByteString.
+     *
+     * @param obj the object to serialize
+     * @return the serialized object as a ByteString
+     */
    public ByteString serialize(JDataVersionedWrapper obj) {
        ByteBuffer buffer = ByteBuffer.allocate(Long.BYTES);
        buffer.putLong(obj.version());
@@ -19,6 +29,13 @@ public class JDataVersionedWrapperSerializer {
        return ByteString.copyFrom(buffer).concat(dataSerializer.serialize(obj.data()));
    }

+    /**
+     * Deserializes a JDataVersionedWrapper object from a ByteBuffer.
+     * Returns a lazy wrapper (JDataVersionedWrapperLazy).
+     *
+     * @param data the ByteBuffer containing the serialized object
+     * @return the deserialized object
+     */
    public JDataVersionedWrapper deserialize(ByteBuffer data) {
        var version = data.getLong();
        return new JDataVersionedWrapperLazy(version, data.remaining(),
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/JObjectKey.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/JObjectKey.java
@@ -5,30 +5,68 @@ import java.nio.ByteBuffer;
 import java.nio.charset.StandardCharsets;
 import java.util.UUID;

+/**
+ * JObjectKey is an interface for object keys to be used in the object store.
+ */
 public sealed interface JObjectKey extends Serializable, Comparable<JObjectKey> permits JObjectKeyImpl, JObjectKeyMax, JObjectKeyMin {
    JObjectKeyMin MIN = new JObjectKeyMin();
    JObjectKeyMax MAX = new JObjectKeyMax();

+    /**
+     * Creates a new JObjectKey from a string value.
+     *
+     * @param value the string value of the key
+     * @return a new JObjectKey
+     */
    static JObjectKey of(String value) {
        return new JObjectKeyImpl(value);
    }

+    /**
+     * Creates a new JObjectKey with a random UUID.
+     *
+     * @return a new JObjectKey with a random UUID
+     */
    static JObjectKey random() {
        return new JObjectKeyImpl(UUID.randomUUID().toString());
    }

+    /**
+     * Returns a JObjectKey that compares less than all other keys.
+     * Calling value on this key will result in an exception.
+     *
+     * @return a JObjectKey that compares less than all other keys
+     */
    static JObjectKey first() {
        return MIN;
    }

+    /**
+     * Returns a JObjectKey that compares greater than all other keys.
+     * Calling value on this key will result in an exception.
+     *
+     * @return a JObjectKey that compares greater than all other keys
+     */
    static JObjectKey last() {
        return MAX;
    }

+    /**
+     * Creates a new JObjectKey from a byte array.
+     *
+     * @param bytes the byte array representing the key
+     * @return a new JObjectKey
+     */
    static JObjectKey fromBytes(byte[] bytes) {
        return new JObjectKeyImpl(new String(bytes, StandardCharsets.ISO_8859_1));
    }

+    /**
+     * Creates a new JObjectKey from a ByteBuffer.
+     *
+     * @param buff the ByteBuffer representing the key
+     * @return a new JObjectKey
+     */
    static JObjectKey fromByteBuffer(ByteBuffer buff) {
        byte[] bytes = new byte[buff.remaining()];
        buff.get(bytes);
@@ -41,7 +79,17 @@ public sealed interface JObjectKey extends Serializable, Comparable<JObjectKey>
    @Override
    String toString();

+    /**
+     * Returns the byte buffer representation of the key.
+     *
+     * @return the byte buffer representation of the key
+     */
    ByteBuffer toByteBuffer();

+    /**
+     * Returns the string value of the key.
+     *
+     * @return the string value of the key
+     */
    String value();
 }
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/JObjectKeyImpl.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/JObjectKeyImpl.java
@@ -7,6 +7,9 @@ import java.nio.ByteBuffer;
 import java.nio.charset.StandardCharsets;
 import java.util.Objects;

+/**
+ * A "real" implementation of JObjectKey, containing an underlying string, and a cached lazily created byte buffer.
+ */
 public final class JObjectKeyImpl implements JObjectKey {
    @Serial
    private static final long serialVersionUID = 0L;
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/JObjectKeyMax.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/JObjectKeyMax.java
@@ -2,6 +2,9 @@ package com.usatiuk.objects;

 import java.nio.ByteBuffer;

+/**
+ * JObjectKey implementation that compares greater than all other keys.
+ */
 public record JObjectKeyMax() implements JObjectKey {
    @Override
    public int compareTo(JObjectKey o) {
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/JObjectKeyMin.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/JObjectKeyMin.java
@@ -2,6 +2,9 @@ package com.usatiuk.objects;

 import java.nio.ByteBuffer;

+/**
+ * JObjectKey implementation that compares less than all other keys.
+ */
 public record JObjectKeyMin() implements JObjectKey {
    @Override
    public int compareTo(JObjectKey o) {
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/JavaDataSerializer.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/JavaDataSerializer.java
@@ -10,6 +10,9 @@ import jakarta.enterprise.context.ApplicationScoped;
 import java.io.IOException;
 import java.nio.ByteBuffer;

+/**
+ * Simple Java object serializer.
+ */
@ApplicationScoped
@DefaultBean
 public class JavaDataSerializer implements ObjectSerializer<JData> {
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/ObjectSerializer.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/ObjectSerializer.java
@@ -4,8 +4,25 @@ import com.google.protobuf.ByteString;

 import java.nio.ByteBuffer;

+/**
+ * Interface for serializing and deserializing objects.
+ *
+ * @param <T> the type of object to serialize/deserialize
+ */
 public interface ObjectSerializer<T> {
+    /**
+     * Serialize an object to a ByteString.
+     *
+     * @param obj the object to serialize
+     * @return the serialized object as a ByteString
+     */
    ByteString serialize(T obj);

+    /**
+     * Deserialize an object from a ByteBuffer.
+     *
+     * @param data the ByteBuffer containing the serialized object
+     * @return the deserialized object
+     */
    T deserialize(ByteBuffer data);
 }
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/CloseableKvIterator.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/CloseableKvIterator.java
@@ -4,19 +4,63 @@ import org.apache.commons.lang3.tuple.Pair;

 import java.util.Iterator;

+
+/**
+ * An iterator over key-value pairs that can be closed and supports peek and skip operations, in both directions.
+ * @param <K> the type of the keys
+ * @param <V> the type of the values
+ */
 public interface CloseableKvIterator<K extends Comparable<? super K>, V> extends Iterator<Pair<K, V>>, AutoCloseable {
+    /**
+     * Returns the upcoming key in the forward direction without advancing the iterator.
+     *
+     * @return the current key
+     * @throws IllegalStateException if there is no next element
+     */
    K peekNextKey();

+    /**
+     * Skips the next element in the forward direction.
+     *
+     * @throws IllegalStateException if there is no next element
+     */
    void skip();

+    /**
+     * Checks if there is a next element in the forward direction.
+     *
+     * @return true if there is a next element, false otherwise
+     * @throws IllegalStateException if there is no next element
+     */
    K peekPrevKey();

+    /**
+     * Returns the key-value pair in the reverse direction, and advances the iterator.
+     *
+     * @return the previous key-value pair
+     * @throws IllegalStateException if there is no previous element
+     */
    Pair<K, V> prev();

+    /**
+     * Checks if there is a previous element in the reverse direction.
+     *
+     * @return true if there is a previous element, false otherwise
+     */
    boolean hasPrev();

+    /**
+     * Skips the previous element in the reverse direction.
+     *
+     * @throws IllegalStateException if there is no previous element
+     */
    void skipPrev();

+    /**
+     * Returns a reversed iterator that iterates in the reverse direction.
+     *
+     * @return a new CloseableKvIterator that iterates in the reverse direction
+     */
    default CloseableKvIterator<K, V> reversed() {
        return new ReversedKvIterator<K, V>(this);
    }
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/Data.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/Data.java
@@ -1,5 +1,13 @@
 package com.usatiuk.objects.iterators;

+/**
+ * Interface indicating that data is present.
+ * @param <V> the type of the value
+ */
 public interface Data<V> extends MaybeTombstone<V> {
+    /**
+     * Get the value.
+     * @return the value
+     */
    V value();
 }
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/DataWrapper.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/DataWrapper.java
@@ -1,4 +1,9 @@
 package com.usatiuk.objects.iterators;

+/**
+ * Simple implementation of the Data interface.
+ * @param value the value
+ * @param <V> the type of the value
+ */
 public record DataWrapper<V>(V value) implements Data<V> {
 }
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/IteratorStart.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/IteratorStart.java
@@ -1,5 +1,8 @@
 package com.usatiuk.objects.iterators;

+/**
+ * Allows to specify initial positioning of the iterator relative to the requested key.
+ */
 public enum IteratorStart {
    LT,
    LE,
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/KeyPredicateKvIterator.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/KeyPredicateKvIterator.java
@@ -5,11 +5,25 @@ import org.apache.commons.lang3.tuple.Pair;
 import java.util.NoSuchElementException;
 import java.util.function.Function;

+/**
+ * A key-value iterator that filters keys based on a predicate.
+ *
+ * @param <K> the type of the keys
+ * @param <V> the type of the values
+ */
 public class KeyPredicateKvIterator<K extends Comparable<K>, V> extends ReversibleKvIterator<K, V> {
    private final CloseableKvIterator<K, V> _backing;
    private final Function<K, Boolean> _filter;
    private K _next;

+    /**
+     * Constructs a KeyPredicateKvIterator with the specified backing iterator, start position, and filter.
+     *
+     * @param backing  the backing iterator
+     * @param start    the starting position relative to the startKey
+     * @param startKey the starting key
+     * @param filter   the filter function to apply to keys. Only keys for which this function returns true will be included in the iteration.
+     */
    public KeyPredicateKvIterator(CloseableKvIterator<K, V> backing, IteratorStart start, K startKey, Function<K, Boolean> filter) {
        _goingForward = true;
        _backing = backing;
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/MappingKvIterator.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/MappingKvIterator.java
@@ -4,10 +4,23 @@ import org.apache.commons.lang3.tuple.Pair;

 import java.util.function.Function;

+/**
+ * A mapping key-value iterator that transforms the values of a backing iterator using a specified function.
+ *
+ * @param <K> the type of the keys
+ * @param <V> the type of the values in the backing iterator
+ * @param <V_T> the type of the transformed values
+ */
 public class MappingKvIterator<K extends Comparable<K>, V, V_T> implements CloseableKvIterator<K, V_T> {
    private final CloseableKvIterator<K, V> _backing;
    private final Function<V, V_T> _transformer;

+    /**
+     * Constructs a MappingKvIterator with the specified backing iterator and transformer function.
+     *
+     * @param backing     the backing iterator
+     * @param transformer the function to transform values
+     */
    public MappingKvIterator(CloseableKvIterator<K, V> backing, Function<V, V_T> transformer) {
        _backing = backing;
        _transformer = transformer;
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/MaybeTombstone.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/MaybeTombstone.java
@@ -1,4 +1,8 @@
 package com.usatiuk.objects.iterators;

+/**
+ * Optional-like interface, can either be {@link Data} or {@link Tombstone}.
+ * @param <T> the type of the value
+ */
 public interface MaybeTombstone<T> {
 }
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/MergingKvIterator.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/MergingKvIterator.java
@@ -9,10 +9,25 @@ import java.util.NavigableMap;
 import java.util.NoSuchElementException;
 import java.util.TreeMap;

+/**
+ * A merging key-value iterator that combines multiple iterators into a single iterator.
+ *
+ * @param <K> the type of the keys
+ * @param <V> the type of the values
+ */
 public class MergingKvIterator<K extends Comparable<K>, V> extends ReversibleKvIterator<K, V> {
    private final NavigableMap<K, IteratorEntry<K, V>> _sortedIterators = new TreeMap<>();
    private final List<IteratorEntry<K, V>> _iterators;

+    /**
+     * Constructs a MergingKvIterator with the specified start type, start key, and list of iterators.
+     * The iterators have priority based on their order in the list: if two iterators have the same key,
+     * the one that is in the beginning of the list will be used.
+     *
+     * @param startType the starting position relative to the startKey
+     * @param startKey  the starting key
+     * @param iterators the list of iterators to merge
+     */
    public MergingKvIterator(IteratorStart startType, K startKey, List<CloseableKvIterator<K, V>> iterators) {
        _goingForward = true;

@@ -88,6 +103,15 @@ public class MergingKvIterator<K extends Comparable<K>, V> extends ReversibleKvI
 //        }
    }

+    /**
+     * Constructs a MergingKvIterator with the specified start type, start key, and array of iterators.
+     * The iterators have priority based on their order in the array: if two iterators have the same key,
+     * the one that is in the beginning of the array will be used.
+     *
+     * @param startType the starting position relative to the startKey
+     * @param startKey  the starting key
+     * @param iterators the array of iterators to merge
+     */
    @SafeVarargs
    public MergingKvIterator(IteratorStart startType, K startKey, CloseableKvIterator<K, V>... iterators) {
        this(startType, startKey, List.of(iterators));
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/NavigableMapKvIterator.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/NavigableMapKvIterator.java
@@ -4,11 +4,25 @@ import org.apache.commons.lang3.tuple.Pair;

 import java.util.*;

+/**
+ * A key-value iterator for a {@link NavigableMap}.
+ * It allows iterating over the keys and values in a sorted order.
+ *
+ * @param <K> the type of the keys
+ * @param <V> the type of the values
+ */
 public class NavigableMapKvIterator<K extends Comparable<K>, V> extends ReversibleKvIterator<K, V> {
    private final NavigableMap<K, V> _map;
    private Iterator<Map.Entry<K, V>> _iterator;
    private Map.Entry<K, V> _next;

+    /**
+     * Constructs a NavigableMapKvIterator with the specified map, start type, and start key.
+     *
+     * @param map   the map to iterate over
+     * @param start the starting position relative to the startKey
+     * @param key   the starting key
+     */
    public NavigableMapKvIterator(NavigableMap<K, ? extends V> map, IteratorStart start, K key) {
        _map = (NavigableMap<K, V>) map;
        SortedMap<K, V> _view;
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/ReversedKvIterator.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/ReversedKvIterator.java
@@ -2,9 +2,19 @@ package com.usatiuk.objects.iterators;

 import org.apache.commons.lang3.tuple.Pair;

+/**
+ * A wrapper for a key-value iterator that iterates in reverse order.
+ * @param <K> the type of the keys
+ * @param <V> the type of the values
+ */
 public class ReversedKvIterator<K extends Comparable<? super K>, V> implements CloseableKvIterator<K, V> {
    private final CloseableKvIterator<K, V> _backing;

+    /**
+     * Constructs a ReversedKvIterator with the specified backing iterator.
+     *
+     * @param backing the backing iterator
+     */
    public ReversedKvIterator(CloseableKvIterator<K, V> backing) {
        _backing = backing;
    }
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/ReversibleKvIterator.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/ReversibleKvIterator.java
@@ -2,9 +2,21 @@ package com.usatiuk.objects.iterators;

 import org.apache.commons.lang3.tuple.Pair;

+/**
+ * Base class for a reversible key-value iterator.
+ *
+ * @param <K> the type of the keys
+ * @param <V> the type of the values
+ */
 public abstract class ReversibleKvIterator<K extends Comparable<K>, V> implements CloseableKvIterator<K, V> {
+    /**
+     * The current direction of the iterator.
+     */
    protected boolean _goingForward;

+    /**
+     * Reverses the current direction of the iterator.
+     */
    protected abstract void reverse();

    private void ensureForward() {
@@ -19,12 +31,33 @@ public abstract class ReversibleKvIterator<K extends Comparable<K>, V> implement
        }
    }

+    /**
+     * Fills the next element in the iterator, depending on the current direction.
+     *
+     * @throws IllegalStateException if there is no next element
+     */
    abstract protected K peekImpl();

+    /**
+     * Skips the next element in the iterator, depending on the current direction.
+     *
+     * @throws IllegalStateException if there is no next element
+     */
    abstract protected void skipImpl();

+    /**
+     * Checks if there is a next element in the iterator, depending on the current direction.
+     *
+     * @return true if there is a next element, false otherwise
+     */
    abstract protected boolean hasImpl();

+    /**
+     * Returns the next element in the iterator, depending on the current direction.
+     *
+     * @return the next element
+     * @throws IllegalStateException if there is no next element
+     */
    abstract protected Pair<K, V> nextImpl();

    @Override
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/Tombstone.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/Tombstone.java
@@ -1,4 +1,8 @@
 package com.usatiuk.objects.iterators;

+/**
+ * Indicates that the value is a tombstone.
+ * @param <V> the type of the value
+ */
 public interface Tombstone<V> extends MaybeTombstone<V> {
 }
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/TombstoneImpl.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/TombstoneImpl.java
@@ -1,4 +1,8 @@
 package com.usatiuk.objects.iterators;

+/**
+ * Simple implementation of the Tombstone interface.
+ * @param <V> the type of the value
+ */
 public record TombstoneImpl<V>() implements Tombstone<V> {
 }
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/TombstoneSkippingIterator.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/iterators/TombstoneSkippingIterator.java
@@ -6,11 +6,25 @@ import java.util.List;
 import java.util.NoSuchElementException;
 import java.util.function.Function;

+/**
+ * A key-value iterator that skips tombstones.
+ *
+ * @param <K> the type of the keys
+ * @param <V> the type of the values
+ */
 public class TombstoneSkippingIterator<K extends Comparable<K>, V> extends ReversibleKvIterator<K, V> {
    private final MergingKvIterator<K, MaybeTombstone<V>> _backing;
    private Pair<K, V> _next = null;
    private boolean _checkedNext = false;

+    /**
+     * Constructs a TombstoneSkippingIterator with the specified start position, start key, and list of iterators.
+     * Like {@link MappingKvIterator}, iterators have a priority depending on their order in the list.
+     *
+     * @param start     the starting position relative to the startKey
+     * @param startKey  the starting key
+     * @param iterators the list of iterators to merge
+     */
    public TombstoneSkippingIterator(IteratorStart start, K startKey, List<CloseableKvIterator<K, MaybeTombstone<V>>> iterators) {
        _goingForward = true;
        _backing = new MergingKvIterator<>(start, startKey, iterators);
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/snapshot/Snapshot.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/snapshot/Snapshot.java
@@ -8,12 +8,36 @@ import javax.annotation.Nonnull;
 import java.util.List;
 import java.util.Optional;

+/**
+ * Interface for a snapshot of a database.
+ * Represents a point-in-time view of a storage, with a unique ID.
+ *
+ * @param <K> the type of the key
+ * @param <V> the type of the value
+ */
 public interface Snapshot<K extends Comparable<K>, V> extends AutoCloseable {
+    /**
+     * Get a list of iterators representing the snapshot.
+     * The iterators have priority: the first one in the list is the highest.
+     * The data type of the iterator is a tombstone: a tombstone represents a deleted value that does not exist anymore.
+     * The list of iterators is intended to be consumed by {@link com.usatiuk.objects.iterators.TombstoneSkippingIterator}
+     *
+     * @return a list of iterators
+     */
    List<CloseableKvIterator<K, MaybeTombstone<V>>> getIterator(IteratorStart start, K key);

+    /**
+     * Read an object from the snapshot.
+     * @param name the name of the object
+     * @return an optional containing the object if it exists, or an empty optional if it does not
+     */
    @Nonnull
    Optional<V> readObject(K name);

+    /**
+     * Get the ID of the snapshot.
+     * @return the ID of the snapshot
+     */
    long id();

    @Override
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/stores/CachingObjectPersistentStore.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/stores/CachingObjectPersistentStore.java
@@ -1,9 +1,12 @@
 package com.usatiuk.objects.stores;

+import com.github.benmanes.caffeine.cache.Caffeine;
 import com.usatiuk.objects.JDataVersionedWrapper;
 import com.usatiuk.objects.JDataVersionedWrapperLazy;
 import com.usatiuk.objects.JObjectKey;
-import com.usatiuk.objects.iterators.*;
+import com.usatiuk.objects.iterators.CloseableKvIterator;
+import com.usatiuk.objects.iterators.IteratorStart;
+import com.usatiuk.objects.iterators.MaybeTombstone;
 import com.usatiuk.objects.snapshot.Snapshot;
 import com.usatiuk.utils.ListUtils;
 import io.quarkus.logging.Log;
@@ -14,123 +17,92 @@ import jakarta.enterprise.event.Observes;
 import jakarta.inject.Inject;
 import org.apache.commons.lang3.tuple.Pair;
 import org.eclipse.microprofile.config.inject.ConfigProperty;
-import org.pcollections.TreePMap;

 import javax.annotation.Nonnull;
+import java.time.Duration;
 import java.util.List;
 import java.util.Optional;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.atomic.AtomicLong;
-import java.util.concurrent.atomic.AtomicReference;

+/**
+ * CachingObjectPersistentStore is a caching layer for the SerializingObjectPersistentStore
+ * It stores the already deserialized objects in memory.
+ * Not (yet) thread safe for writes.
+ */
@ApplicationScoped
 public class CachingObjectPersistentStore {
-    private final AtomicReference<Cache> _cache;
    @Inject
    SerializingObjectPersistentStore delegate;
    @ConfigProperty(name = "dhfs.objects.lru.print-stats")
    boolean printStats;
-    private ExecutorService _statusExecutor;
-    private AtomicLong _cached = new AtomicLong();
-    private AtomicLong _cacheTries = new AtomicLong();
+//    private ExecutorService _statusExecutor;
+
+    private final com.github.benmanes.caffeine.cache.Cache<Pair<Long, JObjectKey>, JDataVersionedWrapper> _cache;

    public CachingObjectPersistentStore(@ConfigProperty(name = "dhfs.objects.lru.limit") int sizeLimit) {
-        _cache = new AtomicReference<>(
-                new Cache(TreePMap.empty(), 0, -1, sizeLimit)
-        );
+        _cache = Caffeine.newBuilder()
+                .maximumWeight(sizeLimit)
+                .weigher((Pair<Long, JObjectKey> key, JDataVersionedWrapper value) -> value.estimateSize())
+                .expireAfterWrite(Duration.ofMinutes(5)).build();
    }

    void init(@Observes @Priority(110) StartupEvent event) {
-        try (var s = delegate.getSnapshot()) {
-            _cache.set(_cache.get().withVersion(s.id()));
-        }
-
-        if (printStats) {
-            _statusExecutor = Executors.newSingleThreadExecutor();
-            _statusExecutor.submit(() -> {
-                try {
-                    while (true) {
-                        Log.infov("Cache status: size=" + _cache.get().size() / 1024 / 1024 + "MB" + " cache success ratio: " + (_cached.get() / (double) _cacheTries.get()));
-                        _cached.set(0);
-                        _cacheTries.set(0);
-                        Thread.sleep(1000);
-                    }
-                } catch (InterruptedException ignored) {
-                }
-            });
-        }
+//        if (printStats) {
+//            _statusExecutor = Executors.newSingleThreadExecutor();
+//            _statusExecutor.submit(() -> {
+//                try {
+//                    while (true) {
+//                        Log.infov("Cache status: size=" + _cache.estimatedSize() / 1024 / 1024 + "MB" + " cache success ratio: " + (_cached.get() / (double) _cacheTries.get()));
+//                        _cached.set(0);
+//                        _cacheTries.set(0);
+//                        Thread.sleep(1000);
+//                    }
+//                } catch (InterruptedException ignored) {
+//                }
+//            });
+//        }
    }

+    /**
+     * Commit the transaction to the underlying store and update the cache.
+     * Once this function returns, the transaction is committed and the cache is updated.
+     *
+     * @param objs the transaction manifest object
+     * @param txId the transaction ID
+     */
    public void commitTx(TxManifestObj<? extends JDataVersionedWrapper> objs, long txId) {
        Log.tracev("Committing: {0} writes, {1} deletes", objs.written().size(), objs.deleted().size());

-        var cache = _cache.get();
-        for (var write : objs.written()) {
-            cache = cache.withPut(write.getLeft(), Optional.of(write.getRight()));
-        }
-        for (var del : objs.deleted()) {
-            cache = cache.withPut(del, Optional.empty());
-        }
-        cache = cache.withVersion(txId);
        delegate.commitTx(objs, txId);
-        _cache.set(cache);

        Log.tracev("Committed: {0} writes, {1} deletes", objs.written().size(), objs.deleted().size());
    }

+    /**
+     * Get a snapshot of underlying store and the cache.
+     * Objects are read from the cache if possible, if not, they are read from the underlying store,
+     * then possibly lazily cached when their data is accessed.
+     *
+     * @return a snapshot of the cached store
+     */
    public Snapshot<JObjectKey, JDataVersionedWrapper> getSnapshot() {
        while (true) {
-            var cache = _cache.get();
-
-            if (cache == null)
-                return delegate.getSnapshot();
-
-            Cache curCache = null;
            Snapshot<JObjectKey, JDataVersionedWrapper> backing = null;

            try {
-                curCache = _cache.get();
                backing = delegate.getSnapshot();

-                if (curCache.version() != backing.id()) {
-                    backing.close();
-                    backing = null;
-                    continue;
-                }
                Snapshot<JObjectKey, JDataVersionedWrapper> finalBacking = backing;
-                Cache finalCurCache = curCache;
                return new Snapshot<JObjectKey, JDataVersionedWrapper>() {
-                    private final Cache _curCache = finalCurCache;
                    private final Snapshot<JObjectKey, JDataVersionedWrapper> _backing = finalBacking;
-                    private boolean _invalid = false;
                    private boolean _closed = false;

-                    private void doCache(JObjectKey key, Optional<JDataVersionedWrapper> obj) {
-                        _cacheTries.incrementAndGet();
-                        if (_invalid)
-                            return;
-
-                        var globalCache = _cache.get();
-                        if (globalCache.version() != _curCache.version()) {
-                            _invalid = true;
-                            return;
-                        }
-
-                        var newCache = globalCache.withPut(key, obj);
-                        if (_cache.compareAndSet(globalCache, newCache))
-                            _cached.incrementAndGet();
+                    private void doCache(JObjectKey key, JDataVersionedWrapper obj) {
+                        var cacheKey = Pair.of(obj.version(), key);
+                        _cache.put(cacheKey, obj);
                    }

-                    private void maybeCache(JObjectKey key, Optional<JDataVersionedWrapper> obj) {
-                        if (obj.isEmpty()) {
-                            doCache(key, obj);
-                            return;
-                        }
-
-                        var wrapper = obj.get();
-
-                        if (!(wrapper instanceof JDataVersionedWrapperLazy lazy)) {
+                    private void maybeCache(JObjectKey key, JDataVersionedWrapper obj) {
+                        if (!(obj instanceof JDataVersionedWrapperLazy lazy)) {
                            doCache(key, obj);
                            return;
                        }
@@ -147,29 +119,25 @@ public class CachingObjectPersistentStore {

                    @Override
                    public List<CloseableKvIterator<JObjectKey, MaybeTombstone<JDataVersionedWrapper>>> getIterator(IteratorStart start, JObjectKey key) {
-                        return ListUtils.prependAndMap(
-                                new NavigableMapKvIterator<JObjectKey, MaybeTombstone<JDataVersionedWrapper>>(_curCache.map(), start, key),
+                        return ListUtils.map(
                                _backing.getIterator(start, key),
                                i -> new CachingKvIterator((CloseableKvIterator<JObjectKey, JDataVersionedWrapper>) (CloseableKvIterator<JObjectKey, ?>) i)
                        );
                    }

+                    private JDataVersionedWrapper tryGetCached(JObjectKey key, JDataVersionedWrapper obj) {
+                        var cached = _cache.getIfPresent(Pair.of(obj.version(), key));
+                        if (cached != null) {
+                            return cached;
+                        }
+                        maybeCache(key, obj);
+                        return obj;
+                    }
+
                    @Nonnull
                    @Override
                    public Optional<JDataVersionedWrapper> readObject(JObjectKey name) {
-                        var cached = _curCache.map().get(name);
-                        if (cached != null) {
-                            return switch (cached) {
-                                case CacheEntryPresent data -> Optional.of(data.value());
-                                case CacheEntryMiss tombstone -> {
-                                    yield Optional.empty();
-                                }
-                                default -> throw new IllegalStateException("Unexpected value: " + cached);
-                            };
-                        }
-                        var read = _backing.readObject(name);
-                        maybeCache(name, read);
-                        return read;
+                        return _backing.readObject(name).map(o -> tryGetCached(name, o));
                    }

                    @Override
@@ -218,8 +186,8 @@ public class CachingObjectPersistentStore {
                        @Override
                        public Pair<JObjectKey, MaybeTombstone<JDataVersionedWrapper>> prev() {
                            var prev = _delegate.prev();
-                            maybeCache(prev.getKey(), Optional.of(prev.getValue()));
-                            return (Pair<JObjectKey, MaybeTombstone<JDataVersionedWrapper>>) (Pair<JObjectKey, ?>) prev;
+                            var cached = tryGetCached(prev.getKey(), prev.getValue());
+                            return Pair.of(prev.getKey(), cached);
                        }

                        @Override
@@ -235,8 +203,8 @@ public class CachingObjectPersistentStore {
                        @Override
                        public Pair<JObjectKey, MaybeTombstone<JDataVersionedWrapper>> next() {
                            var next = _delegate.next();
-                            maybeCache(next.getKey(), Optional.of(next.getValue()));
-                            return (Pair<JObjectKey, MaybeTombstone<JDataVersionedWrapper>>) (Pair<JObjectKey, ?>) next;
+                            var cached = tryGetCached(next.getKey(), next.getValue());
+                            return Pair.of(next.getKey(), cached);
                        }
                    }
                };
@@ -248,54 +216,4 @@ public class CachingObjectPersistentStore {
            }
        }
    }
-
-    private interface CacheEntry extends MaybeTombstone<JDataVersionedWrapper> {
-        int size();
-    }
-
-    private record Cache(TreePMap<JObjectKey, CacheEntry> map,
-                         int size,
-                         long version,
-                         int sizeLimit) {
-        public Cache withPut(JObjectKey key, Optional<JDataVersionedWrapper> obj) {
-            var entry = obj.<CacheEntry>map(o -> new CacheEntryPresent(o, o.estimateSize())).orElse(new CacheEntryMiss());
-
-            int newSize = size() + entry.size();
-
-            var old = map.get(key);
-            if (old != null)
-                newSize -= old.size();
-
-            TreePMap<JObjectKey, CacheEntry> newCache = map();
-
-            while (newSize > sizeLimit) {
-                var del = newCache.firstEntry();
-                newCache = newCache.minusFirstEntry();
-                newSize -= del.getValue().size();
-            }
-
-            newCache = newCache.plus(key, entry);
-            return new Cache(
-                    newCache,
-                    newSize,
-                    version,
-                    sizeLimit
-            );
-        }
-
-        public Cache withVersion(long version) {
-            return new Cache(map, size, version, sizeLimit);
-        }
-    }
-
-    private record CacheEntryPresent(JDataVersionedWrapper value,
-                                     int size) implements CacheEntry, Data<JDataVersionedWrapper> {
-    }
-
-    private record CacheEntryMiss() implements CacheEntry, Tombstone<JDataVersionedWrapper> {
-        @Override
-        public int size() {
-            return 64;
-        }
-    }
 }
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/stores/LmdbObjectPersistentStore.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/stores/LmdbObjectPersistentStore.java
@@ -26,15 +26,19 @@ import java.nio.file.Path;
 import java.util.List;
 import java.util.NoSuchElementException;
 import java.util.Optional;
-import java.util.stream.Stream;

 import static org.lmdbjava.DbiFlags.MDB_CREATE;
 import static org.lmdbjava.Env.create;

+/**
+ * Persistent object storage using LMDB
+ */
@ApplicationScoped
@IfBuildProperty(name = "dhfs.objects.persistence", stringValue = "lmdb")
 public class LmdbObjectPersistentStore implements ObjectPersistentStore {
    private static final String DB_NAME = "objects";
+
+    // LMDB object name for the transaction id
    private static final String DB_VER_OBJ_NAME_STR = "__DB_VER_OBJ";
    private static final ByteBuffer DB_VER_OBJ_NAME;

@@ -54,7 +58,7 @@ public class LmdbObjectPersistentStore implements ObjectPersistentStore {
    private Dbi<ByteBuffer> _db;
    private boolean _ready = false;

-    public LmdbObjectPersistentStore(@ConfigProperty(name = "dhfs.objects.persistence.files.root") String root) {
+    public LmdbObjectPersistentStore(@ConfigProperty(name = "dhfs.objects.persistence.root") String root) {
        _root = Path.of(root).resolve("objects");
    }

@@ -63,12 +67,15 @@ public class LmdbObjectPersistentStore implements ObjectPersistentStore {
            Log.info("Initializing with root " + _root);
            _root.toFile().mkdirs();
        }
+        Log.info("Opening LMDB with root " + _root);
        _env = create()
                .setMapSize(lmdbSize)
                .setMaxDbs(1)
                .open(_root.toFile(), EnvFlags.MDB_NOTLS);
        _db = _env.openDbi(DB_NAME, MDB_CREATE);

+        Log.info("Opened LMDB with root " + _root);
+
        try (Txn<ByteBuffer> txn = _env.txnWrite()) {
            var read = readTxId(txn);
            if (read.isPresent()) {
@@ -83,6 +90,7 @@ public class LmdbObjectPersistentStore implements ObjectPersistentStore {
        }

        _ready = true;
+        Log.info("LMDB storage ready");
    }

    private Optional<Long> readTxId(Txn<ByteBuffer> txn) {
@@ -91,6 +99,9 @@ public class LmdbObjectPersistentStore implements ObjectPersistentStore {
    }

    void shutdown(@Observes @Priority(900) ShutdownEvent event) throws IOException {
+        if (!_ready) {
+            return;
+        }
        _ready = false;
        _db.close();
        _env.close();
@@ -100,8 +111,15 @@ public class LmdbObjectPersistentStore implements ObjectPersistentStore {
        if (!_ready) throw new IllegalStateException("Wrong service order!");
    }

+    /**
+     * Get a snapshot of the database.
+     * Note that the ByteBuffers are invalid after the snapshot is closed.
+     *
+     * @return a snapshot of the database
+     */
    @Override
    public Snapshot<JObjectKey, ByteBuffer> getSnapshot() {
+        verifyReady();
        var txn = _env.txnRead();
        try {
            long commitId = readTxId(txn).orElseThrow();
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/stores/MemoryObjectPersistentStore.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/stores/MemoryObjectPersistentStore.java
@@ -15,6 +15,10 @@ import java.util.Optional;
 import java.util.concurrent.locks.ReentrantReadWriteLock;
 import java.util.stream.Stream;

+/**
+ * In-memory implementation of the ObjectPersistentStore interface.
+ * For testing purposes.
+ */
@ApplicationScoped
@IfBuildProperty(name = "dhfs.objects.persistence", stringValue = "memory")
 public class MemoryObjectPersistentStore implements ObjectPersistentStore {
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/stores/ObjectPersistentStore.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/stores/ObjectPersistentStore.java
@@ -8,14 +8,33 @@ import javax.annotation.Nonnull;
 import java.nio.ByteBuffer;
 import java.util.Optional;

-// Persistent storage of objects
-// All changes are written as sequential transactions
+/**
+ * Interface for a persistent store of objects.
+ * Does not have to be thread-safe! (yet), it is expected that all commits are done by the same thread.
+ */
 public interface ObjectPersistentStore {
+    /**
+     * Get a snapshot of the persistent store.
+     * @return a snapshot of the persistent store
+     */
    Snapshot<JObjectKey, ByteBuffer> getSnapshot();

+    /**
+     * Commit a transaction to the persistent store.
+     * @param names the transaction manifest
+     * @param txId the transaction ID
+     */
    void commitTx(TxManifestRaw names, long txId);

+    /**
+     * Get the size of the persistent store.
+     * @return the size of the persistent store
+     */
    long getTotalSpace();

+    /**
+     * Get the free space of the persistent store.
+     * @return the free space of the persistent store
+     */
    long getFreeSpace();
 }
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/stores/SerializingObjectPersistentStore.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/stores/SerializingObjectPersistentStore.java
@@ -16,6 +16,11 @@ import java.util.List;
 import java.util.Optional;
 import java.util.stream.Stream;

+/**
+ * Serializing wrapper for the ObjectPersistentStore.
+ * It serializes the objects before storing them in the persistent store.
+ * It deserializes the objects after reading them from the persistent store.
+ */
@ApplicationScoped
 public class SerializingObjectPersistentStore {
    @Inject
@@ -24,6 +29,13 @@ public class SerializingObjectPersistentStore {
    @Inject
    ObjectPersistentStore delegateStore;

+    /**
+     * Get a snapshot of the persistent store, with deserialized objects.
+     *
+     * The objects are deserialized lazily, only when their data is accessed.
+     *
+     * @return a snapshot of the persistent store
+     */
    public Snapshot<JObjectKey, JDataVersionedWrapper> getSnapshot() {
        return new Snapshot<JObjectKey, JDataVersionedWrapper>() {
            private final Snapshot<JObjectKey, ByteBuffer> _backing = delegateStore.getSnapshot();
@@ -54,6 +66,12 @@ public class SerializingObjectPersistentStore {

    }

+
+    /**
+     * Serialize the objects, in parallel
+     * @param objs the objects to serialize
+     * @return the serialized objects
+     */
    private TxManifestRaw prepareManifest(TxManifestObj<? extends JDataVersionedWrapper> objs) {
        return new TxManifestRaw(
                objs.written().parallelStream()
@@ -62,6 +80,11 @@ public class SerializingObjectPersistentStore {
                , objs.deleted());
    }

+    /**
+     * Commit a transaction to the persistent store.
+     * @param objects the transaction manifest
+     * @param txId the transaction ID
+     */
    void commitTx(TxManifestObj<? extends JDataVersionedWrapper> objects, long txId) {
        delegateStore.commitTx(prepareManifest(objects), txId);
    }
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/stores/TxManifestObj.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/stores/TxManifestObj.java
@@ -6,7 +6,6 @@ import org.apache.commons.lang3.tuple.Pair;
 import java.io.Serializable;
 import java.util.Collection;

-// FIXME: Serializable
 public record TxManifestObj<T>(Collection<Pair<JObjectKey, T>> written,
                               Collection<JObjectKey> deleted) implements Serializable {
 }
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/stores/TxManifestRaw.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/stores/TxManifestRaw.java
@@ -7,7 +7,6 @@ import org.apache.commons.lang3.tuple.Pair;
 import java.io.Serializable;
 import java.util.Collection;

-// FIXME: Serializable
 public record TxManifestRaw(Collection<Pair<JObjectKey, ByteString>> written,
                            Collection<JObjectKey> deleted) implements Serializable {
 }
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/stores/WritebackObjectPersistentStore.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/stores/WritebackObjectPersistentStore.java
@@ -33,6 +33,10 @@ import java.util.concurrent.locks.Condition;
 import java.util.concurrent.locks.ReentrantLock;
 import java.util.function.Consumer;

+/**
+ * Asynchronous write cache of objects.
+ * Objects are put into a write queue by commitTx, and written to the storage by a separate thread.
+ */
@ApplicationScoped
 public class WritebackObjectPersistentStore {
    @Inject
@@ -260,16 +264,23 @@ public class WritebackObjectPersistentStore {
        }
    }

-    public void asyncFence(long bundleId, Runnable fn) {
+    /**
+     * Run a given callback after the transaction with id txId is committed.
+     * If the transaction is already committed, the callback is run immediately.
+     *
+     * @param txId transaction id to wait for
+     * @param fn   callback to run
+     */
+    public void asyncFence(long txId, Runnable fn) {
        verifyReady();
-        if (bundleId < 0) throw new IllegalArgumentException("txId should be >0!");
-        if (_lastFlushedId.get() >= bundleId) {
+        if (txId < 0) throw new IllegalArgumentException("txId should be >0!");
+        if (_lastFlushedId.get() >= txId) {
            fn.run();
            return;
        }
        _pendingBundleLock.lock();
        try {
-            if (_lastFlushedId.get() >= bundleId) {
+            if (_lastFlushedId.get() >= txId) {
                fn.run();
                return;
            }
@@ -284,12 +295,32 @@ public class WritebackObjectPersistentStore {
        }
    }

+    /**
+     * Commit a transaction to the persistent store.
+     *
+     * @param writes the transaction manifest
+     * @return a function that allows to add a callback to be run after the transaction is committed
+     */
    public Consumer<Runnable> commitTx(Collection<TxRecord.TxObjectRecord<?>> writes) {
        long bundleId = commitBundle(writes);

        return r -> asyncFence(bundleId, r);
    }

+    /**
+     * Get the last committed transaction ID.
+     *
+     * @return the last committed transaction ID
+     */
+    public long getLastCommitId() {
+        return _lastCommittedId.get();
+    }
+
+    /**
+     * Get a snapshot of the persistent store, including the pending writes.
+     *
+     * @return a snapshot of the store
+     */
    public Snapshot<JObjectKey, JDataVersionedWrapper> getSnapshot() {
        Snapshot<JObjectKey, JDataVersionedWrapper> cache = null;
        PendingWriteData pw = null;
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/transaction/TransactionImpl.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/transaction/TransactionImpl.java
@@ -23,14 +23,16 @@ class TransactionImpl implements Transaction, AutoCloseable {
    private boolean _writeTrack = false;
    private Map<JObjectKey, TxRecord.TxObjectRecord<?>> _newWrites = new HashMap<>();

-    private interface ReadTrackingInternalCrap {
+    /**
+     * Identifies the source of the read: whether it's from the source or written from the transaction.
+     */
+    private interface ReadTrackingSourceWrapper {
        boolean fromSource();

        JData obj();
    }

-    // FIXME:
-    private record ReadTrackingInternalCrapSource(JDataVersionedWrapper wrapped) implements ReadTrackingInternalCrap {
+    private record ReadTrackingSourceWrapperSource(JDataVersionedWrapper wrapped) implements ReadTrackingSourceWrapper {
        @Override
        public boolean fromSource() {
            return true;
@@ -42,7 +44,7 @@ class TransactionImpl implements Transaction, AutoCloseable {
        }
    }

-    private record ReadTrackingInternalCrapTx(JData obj) implements ReadTrackingInternalCrap {
+    private record ReadTrackingSourceWrapperTx(JData obj) implements ReadTrackingSourceWrapper {
        @Override
        public boolean fromSource() {
            return false;
@@ -107,21 +109,21 @@ class TransactionImpl implements Transaction, AutoCloseable {
    @Override
    public CloseableKvIterator<JObjectKey, JData> getIterator(IteratorStart start, JObjectKey key) {
        Log.tracev("Getting tx iterator with start={0}, key={1}", start, key);
-        return new ReadTrackingIterator(new TombstoneSkippingIterator<JObjectKey, ReadTrackingInternalCrap>(start, key,
+        return new ReadTrackingIterator(new TombstoneSkippingIterator<JObjectKey, ReadTrackingSourceWrapper>(start, key,
                ListUtils.prependAndMap(
                        new MappingKvIterator<>(new NavigableMapKvIterator<>(_writes, start, key),
                                t -> switch (t) {
                                    case TxRecord.TxObjectRecordWrite<?> write ->
-                                            new DataWrapper<ReadTrackingInternalCrap>(new ReadTrackingInternalCrapTx(write.data()));
+                                            new DataWrapper<ReadTrackingSourceWrapper>(new ReadTrackingSourceWrapperTx(write.data()));
                                    case TxRecord.TxObjectRecordDeleted deleted ->
-                                            new TombstoneImpl<ReadTrackingInternalCrap>();
+                                            new TombstoneImpl<ReadTrackingSourceWrapper>();
                                    case null, default -> null;
                                }),
                        _snapshot.getIterator(start, key),
-                        itin -> new MappingKvIterator<JObjectKey, MaybeTombstone<JDataVersionedWrapper>, MaybeTombstone<ReadTrackingInternalCrap>>(itin,
+                        itin -> new MappingKvIterator<JObjectKey, MaybeTombstone<JDataVersionedWrapper>, MaybeTombstone<ReadTrackingSourceWrapper>>(itin,
                                d -> switch (d) {
                                    case Data<JDataVersionedWrapper> w ->
-                                            new DataWrapper<>(new ReadTrackingInternalCrapSource(w.value()));
+                                            new DataWrapper<>(new ReadTrackingSourceWrapperSource(w.value()));
                                    case Tombstone<JDataVersionedWrapper> t -> new TombstoneImpl<>();
                                    case null, default -> null;
                                }))));
@@ -178,9 +180,9 @@ class TransactionImpl implements Transaction, AutoCloseable {
    }

    private class ReadTrackingIterator implements CloseableKvIterator<JObjectKey, JData> {
-        private final CloseableKvIterator<JObjectKey, ReadTrackingInternalCrap> _backing;
+        private final CloseableKvIterator<JObjectKey, ReadTrackingSourceWrapper> _backing;

-        public ReadTrackingIterator(CloseableKvIterator<JObjectKey, ReadTrackingInternalCrap> backing) {
+        public ReadTrackingIterator(CloseableKvIterator<JObjectKey, ReadTrackingSourceWrapper> backing) {
            _backing = backing;
        }

@@ -202,7 +204,7 @@ class TransactionImpl implements Transaction, AutoCloseable {
        @Override
        public Pair<JObjectKey, JData> prev() {
            var got = _backing.prev();
-            if (got.getValue() instanceof ReadTrackingInternalCrapSource(JDataVersionedWrapper wrapped)) {
+            if (got.getValue() instanceof ReadTrackingSourceWrapperSource(JDataVersionedWrapper wrapped)) {
                _readSet.putIfAbsent(got.getKey(), Optional.of(wrapped));
            }
            return Pair.of(got.getKey(), got.getValue().obj());
@@ -231,7 +233,7 @@ class TransactionImpl implements Transaction, AutoCloseable {
        @Override
        public Pair<JObjectKey, JData> next() {
            var got = _backing.next();
-            if (got.getValue() instanceof ReadTrackingInternalCrapSource(JDataVersionedWrapper wrapped)) {
+            if (got.getValue() instanceof ReadTrackingSourceWrapperSource(JDataVersionedWrapper wrapped)) {
                _readSet.putIfAbsent(got.getKey(), Optional.of(wrapped));
            }
            return Pair.of(got.getKey(), got.getValue().obj());
--- a/dhfs-parent/objects/src/main/java/com/usatiuk/objects/transaction/TransactionService.java
+++ b/dhfs-parent/objects/src/main/java/com/usatiuk/objects/transaction/TransactionService.java
@@ -165,7 +165,6 @@ public class TransactionService {
                    toUnlock.add(lock);
                }

-                commitSnapshot = writebackObjectPersistentStore.getSnapshot();
            } else {
                Log.trace("Committing transaction - no changes");

@@ -201,7 +200,10 @@ public class TransactionService {
            Log.trace("Committing transaction start");
            var snapshotId = tx.snapshot().id();

-            if (snapshotId != commitSnapshot.id()) {
+            // All dependencies are locked and could not be changed concurrently now
+            if (snapshotId != writebackObjectPersistentStore.getLastCommitId()) {
+                commitSnapshot = writebackObjectPersistentStore.getSnapshot();
+
                for (var read : readSet.entrySet()) {
                    var current = commitSnapshot.readObject(read.getKey());

--- a/dhfs-parent/objects/src/main/resources/application.properties
+++ b/dhfs-parent/objects/src/main/resources/application.properties
@@ -3,7 +3,7 @@ dhfs.objects.writeback.limit=16777216
 dhfs.objects.lru.limit=67108864
 dhfs.objects.lru.print-stats=false
 dhfs.objects.lock_timeout_secs=15
-dhfs.objects.persistence.files.root=${HOME}/dhfs_default/data/objs
+dhfs.objects.persistence.root=${HOME}/dhfs_default/data/objs
 dhfs.objects.persistence.snapshot-extra-checks=false
 dhfs.objects.last-seen.update=60
 dhfs.objects.last-seen.timeout=43200
--- a/dhfs-parent/objects/src/test/java/com/usatiuk/objects/TempDataProfile.java
+++ b/dhfs-parent/objects/src/test/java/com/usatiuk/objects/TempDataProfile.java
@@ -21,7 +21,7 @@ public class TempDataProfile implements QuarkusTestProfile {
            throw new RuntimeException(e);
        }
        var ret = new HashMap<String, String>();
-        ret.put("dhfs.objects.persistence.files.root", tempDirWithPrefix.resolve("dhfs_root_test").toString());
+        ret.put("dhfs.objects.persistence.root", tempDirWithPrefix.resolve("dhfs_root_test").toString());
        ret.put("dhfs.fuse.root", tempDirWithPrefix.resolve("dhfs_fuse_root_test").toString());
        ret.put("dhfs.objects.persistence", "lmdb");
        getConfigOverrides(ret);
--- a/dhfs-parent/objects/src/test/java/com/usatiuk/objects/TestDataCleaner.java
+++ b/dhfs-parent/objects/src/test/java/com/usatiuk/objects/TestDataCleaner.java
@@ -15,7 +15,7 @@ import java.util.Objects;

@ApplicationScoped
 public class TestDataCleaner {
-    @ConfigProperty(name = "dhfs.objects.persistence.files.root")
+    @ConfigProperty(name = "dhfs.objects.persistence.root")
    String tempDirectory;

    void init(@Observes @Priority(1) StartupEvent event) throws IOException {
--- a/dhfs-parent/pom.xml
+++ b/dhfs-parent/pom.xml
@@ -28,8 +28,8 @@
        <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
        <quarkus.platform.artifact-id>quarkus-bom</quarkus.platform.artifact-id>
        <quarkus.platform.group-id>io.quarkus.platform</quarkus.platform.group-id>
-        <quarkus.platform.version>3.20.0</quarkus.platform.version>
-        <surefire-plugin.version>3.5.2</surefire-plugin.version>
+        <quarkus.platform.version>3.27.0</quarkus.platform.version>
+        <surefire-plugin.version>3.5.4</surefire-plugin.version>
        <dhfs.native-libs-dir>${project.parent.build.outputDirectory}/native</dhfs.native-libs-dir>
    </properties>

@@ -54,11 +54,6 @@
                <version>1.18.34</version>
                <scope>provided</scope>
            </dependency>
-            <dependency>
-                <groupId>net.openhft</groupId>
-                <artifactId>zero-allocation-hashing</artifactId>
-                <version>0.16</version>
-            </dependency>
            <dependency>
                <groupId>org.awaitility</groupId>
                <artifactId>awaitility</artifactId>
@@ -68,7 +63,7 @@
            <dependency>
                <groupId>org.junit.jupiter</groupId>
                <artifactId>junit-jupiter-engine</artifactId>
-                <version>5.9.1</version>
+                <version>5.13.4</version>
                <scope>test</scope>
            </dependency>
            <dependency>
--- a/dhfs-parent/sync-base/docker-compose.yml
+++ b/dhfs-parent/sync-base/docker-compose.yml
@@ -1,43 +0,0 @@
-version: "3.2"
-
-services:
-  dhfs1:
-    build: .
-    privileged: true
-    devices:
-      - /dev/fuse
-    volumes:
-      - $HOME/dhfs/dhfs1:/dhfs_root
-      - $HOME/dhfs/dhfs1_f:/dhfs_root/fuse:rshared
-      - ./target/quarkus-app:/app
-    command: "java --add-exports java.base/sun.nio.ch=ALL-UNNAMED
-     -Ddhfs.objects.persistence.files.root=/dhfs_root/p 
-     -Ddhfs.objects.root=/dhfs_root/d 
-     -Ddhfs.fuse.root=/dhfs_root/fuse -Dquarkus.http.host=0.0.0.0 
-     -agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=*:5005
-     -jar /app/quarkus-run.jar"
-    ports:
-      - 8080:8080
-      - 8081:8443
-      - 5005:5005
-  dhfs2:
-    build: .
-    privileged: true
-    devices:
-      - /dev/fuse
-    volumes:
-      - $HOME/dhfs/dhfs2:/dhfs_root
-      - $HOME/dhfs/dhfs2_f:/dhfs_root/fuse:rshared
-      - ./target/quarkus-app:/app
-    command: "java --add-exports java.base/sun.nio.ch=ALL-UNNAMED
-     --add-exports java.base/jdk.internal.access=ALL-UNNAMED
-     --add-opens=java.base/java.nio=ALL-UNNAMED
-     -Ddhfs.objects.persistence.files.root=/dhfs_root/p 
-     -Ddhfs.objects.root=/dhfs_root/d 
-     -Ddhfs.fuse.root=/dhfs_root/fuse -Dquarkus.http.host=0.0.0.0
-     -agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=*:5010
-     -jar /app/quarkus-run.jar"
-    ports:
-      - 8090:8080
-      - 8091:8443
-      - 5010:5010
--- a/dhfs-parent/sync-base/pom.xml
+++ b/dhfs-parent/sync-base/pom.xml
@@ -13,10 +13,6 @@
    </parent>

    <dependencies>
-        <dependency>
-            <groupId>io.quarkus</groupId>
-            <artifactId>quarkus-smallrye-openapi</artifactId>
-        </dependency>
        <dependency>
            <groupId>org.testcontainers</groupId>
            <artifactId>testcontainers</artifactId>
@@ -39,10 +35,6 @@
            <groupId>io.quarkus</groupId>
            <artifactId>quarkus-security</artifactId>
        </dependency>
-        <dependency>
-            <groupId>net.openhft</groupId>
-            <artifactId>zero-allocation-hashing</artifactId>
-        </dependency>
        <dependency>
            <groupId>io.quarkus</groupId>
            <artifactId>quarkus-grpc</artifactId>
@@ -59,14 +51,6 @@
            <groupId>io.quarkus</groupId>
            <artifactId>quarkus-rest-client</artifactId>
        </dependency>
-        <dependency>
-            <groupId>io.quarkus</groupId>
-            <artifactId>quarkus-rest-client-jsonb</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>io.quarkus</groupId>
-            <artifactId>quarkus-rest-jsonb</artifactId>
-        </dependency>
        <dependency>
            <groupId>io.quarkus</groupId>
            <artifactId>quarkus-scheduler</artifactId>
@@ -101,11 +85,6 @@
            <groupId>org.pcollections</groupId>
            <artifactId>pcollections</artifactId>
        </dependency>
-        <dependency>
-            <groupId>org.apache.commons</groupId>
-            <artifactId>commons-math3</artifactId>
-            <version>3.6.1</version>
-        </dependency>
        <dependency>
            <groupId>com.usatiuk</groupId>
            <artifactId>kleppmanntree</artifactId>
--- a/dhfs-parent/sync-base/src/main/java/com/usatiuk/dhfs/DeadlockDetector.java
+++ b/dhfs-parent/sync-base/src/main/java/com/usatiuk/dhfs/DeadlockDetector.java
@@ -1,3 +1,5 @@
+package com.usatiuk.dhfs;
+
 import io.quarkus.logging.Log;
 import io.quarkus.runtime.ShutdownEvent;
 import io.quarkus.runtime.StartupEvent;
@@ -12,6 +14,9 @@ import java.util.Arrays;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;

+/**
+ * Periodically check for deadlocks in the JVM and log them if found.
+ */
@ApplicationScoped
 public class DeadlockDetector {
    private final ExecutorService _executor = Executors.newSingleThreadExecutor();
--- a/dhfs-parent/sync-base/src/main/java/com/usatiuk/dhfs/TemporaryOpSerializer.java
+++ b/dhfs-parent/sync-base/src/main/java/com/usatiuk/dhfs/TemporaryOpSerializer.java
@@ -6,7 +6,7 @@ import com.usatiuk.utils.SerializationHelper;
 import jakarta.inject.Singleton;

@Singleton
-public class TemporaryOpSerializer implements ProtoSerializer<OpP, Op> {
+public class OpSerializer implements ProtoSerializer<OpP, Op> {
    @Override
    public Op deserialize(OpP message) {
        return SerializationHelper.deserialize(message.getSerializedData().toByteArray());
--- a/dhfs-parent/sync-base/src/main/java/com/usatiuk/dhfs/ShutdownChecker.java
+++ b/dhfs-parent/sync-base/src/main/java/com/usatiuk/dhfs/ShutdownChecker.java
@@ -11,10 +11,15 @@ import org.eclipse.microprofile.config.inject.ConfigProperty;
 import java.io.IOException;
 import java.nio.file.Paths;

+/**
+ * This class checks if the application was shut down cleanly.
+ * It creates a file in the specified directory on startup and deletes it on shutdown.
+ * If the file exists on startup, it means the application was not shut down cleanly.
+ */
@ApplicationScoped
 public class ShutdownChecker {
    private static final String dataFileName = "running";
-    @ConfigProperty(name = "dhfs.objects.persistence.files.root")
+    @ConfigProperty(name = "dhfs.objects.persistence.root")
    String dataRoot;
    boolean _cleanShutdown = true;
    boolean _initialized = false;
--- a/dhfs-parent/sync-base/src/main/java/com/usatiuk/dhfs/autosync/AutosyncProcessor.java
+++ b/dhfs-parent/sync-base/src/main/java/com/usatiuk/dhfs/autosync/AutosyncProcessor.java
@@ -22,6 +22,9 @@ import org.eclipse.microprofile.config.inject.ConfigProperty;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;

+/**
+ * Simple class to automatically download remote objects in the background.
+ */
@ApplicationScoped
 public class AutosyncProcessor {
    private final HashSetDelayedBlockingQueue<JObjectKey> _pending = new HashSetDelayedBlockingQueue<>(0);
@@ -77,6 +80,11 @@ public class AutosyncProcessor {
        _autosyncExcecutor.shutdownNow();
    }

+    /**
+     * Adds an object to the queue to be downloaded.
+     *
+     * @param name the object to add
+     */
    public void add(JObjectKey name) {
        _pending.add(name);
    }
--- a/dhfs-parent/sync-base/src/main/java/com/usatiuk/dhfs/autosync/AutosyncTxHook.java
+++ b/dhfs-parent/sync-base/src/main/java/com/usatiuk/dhfs/autosync/AutosyncTxHook.java
@@ -10,6 +10,9 @@ import jakarta.inject.Inject;
 import jakarta.inject.Singleton;
 import org.eclipse.microprofile.config.inject.ConfigProperty;

+/**
+ * Pre-commit hook to automatically download remote objects, if the option to download all objects is enabled.
+ */
@Singleton
 public class AutosyncTxHook implements PreCommitTxHook {
    @Inject
--- a/dhfs-parent/sync-base/src/main/java/com/usatiuk/dhfs/invalidation/DeferredInvalidationQueueData.java
+++ b/dhfs-parent/sync-base/src/main/java/com/usatiuk/dhfs/invalidation/DeferredInvalidationQueueData.java
@@ -7,6 +7,9 @@ import org.apache.commons.collections4.multimap.HashSetValuedHashMap;
 import java.io.Serial;
 import java.io.Serializable;

+/**
+ * Stores data about deferred invalidations.
+ */
 public class DeferredInvalidationQueueData implements Serializable {
    @Serial
    private static final long serialVersionUID = 1L;
--- a/dhfs-parent/sync-base/src/main/java/com/usatiuk/dhfs/invalidation/DeferredInvalidationQueueService.java
+++ b/dhfs-parent/sync-base/src/main/java/com/usatiuk/dhfs/invalidation/DeferredInvalidationQueueService.java
@@ -20,6 +20,11 @@ import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Paths;

+/**
+ * Service to handle deferred invalidations.
+ * It is responsible for storing and returning deferred invalidations to the invalidation queue.
+ * It also is responsible for persisting and restoring the deferred invalidations on startup and shutdown.
+ */
@ApplicationScoped
 public class DeferredInvalidationQueueService implements PeerConnectedEventListener {
    private static final String dataFileName = "invqueue";
@@ -27,7 +32,7 @@ public class DeferredInvalidationQueueService implements PeerConnectedEventListe
    ReachablePeerManager reachablePeerManager;
    @Inject
    InvalidationQueueService invalidationQueueService;
-    @ConfigProperty(name = "dhfs.objects.persistence.files.root")
+    @ConfigProperty(name = "dhfs.objects.persistence.root")
    String dataRoot;
    private DeferredInvalidationQueueData _persistentData = new DeferredInvalidationQueueData();

@@ -59,14 +64,21 @@ public class DeferredInvalidationQueueService implements PeerConnectedEventListe
        }
    }

-    // FIXME:
-    @Scheduled(every = "15s", concurrentExecution = Scheduled.ConcurrentExecution.SKIP)
+    /**
+     * Periodically returns deferred invalidations to the invalidation queue for all reachable hosts.
+     */
+    @Scheduled(every = "15s", concurrentExecution = Scheduled.ConcurrentExecution.SKIP, skipExecutionIf = Scheduled.ApplicationNotRunning.class)
    @Blocking
    void periodicReturn() {
        for (var reachable : reachablePeerManager.getAvailableHosts())
            returnForHost(reachable);
    }

+    /**
+     * Returns deferred invalidations for a specific host.
+     *
+     * @param host the host to return deferred invalidations for
+     */
    void returnForHost(PeerId host) {
        synchronized (this) {
            var col = _persistentData.deferredInvalidations.get(host);
@@ -78,6 +90,10 @@ public class DeferredInvalidationQueueService implements PeerConnectedEventListe
        }
    }

+    /**
+     * Defer a specific invalidation.
+     * @param entry the invalidation to defer
+     */
    void defer(InvalidationQueueEntry entry) {
        synchronized (this) {
            Log.tracev("Deferred invalidation: {0}", entry);
--- a/dhfs-parent/sync-base/src/main/java/com/usatiuk/dhfs/invalidation/IndexUpdateOp.java
+++ b/dhfs-parent/sync-base/src/main/java/com/usatiuk/dhfs/invalidation/IndexUpdateOp.java
@@ -8,6 +8,12 @@ import org.pcollections.PMap;
 import java.util.Collection;
 import java.util.List;

+/**
+ * Information about a new version of a remote object, possibly with its data.
+ * @param key the key of the object
+ * @param changelog the changelog of the object (version vector)
+ * @param data the data of the object
+ */
 public record IndexUpdateOp(JObjectKey key, PMap<PeerId, Long> changelog, JDataRemoteDto data) implements Op {
    @Override
    public Collection<JObjectKey> getEscapedRefs() {
--- a/dhfs-parent/sync-base/src/main/java/com/usatiuk/dhfs/invalidation/InvalidationQueueService.java
+++ b/dhfs-parent/sync-base/src/main/java/com/usatiuk/dhfs/invalidation/InvalidationQueueService.java
@@ -2,8 +2,8 @@ package com.usatiuk.dhfs.invalidation;

 import com.usatiuk.dhfs.peersync.PeerId;
 import com.usatiuk.dhfs.peersync.PeerInfoService;
-import com.usatiuk.dhfs.peersync.ReachablePeerManager;
 import com.usatiuk.dhfs.peersync.PersistentPeerDataService;
+import com.usatiuk.dhfs.peersync.ReachablePeerManager;
 import com.usatiuk.dhfs.rpc.RemoteObjectServiceClient;
 import com.usatiuk.objects.JData;
 import com.usatiuk.objects.JObjectKey;
@@ -31,6 +31,11 @@ import java.util.concurrent.Executors;
 import java.util.concurrent.TimeUnit;
 import java.util.concurrent.atomic.AtomicReference;

+/**
+ * Service to handle sending operations to remote peers.
+ * This service works with objects, containing a queue of them.
+ * The operations to be sent to peers are extracted from the objects in the queue.
+ */
@ApplicationScoped
 public class InvalidationQueueService {
    private final HashSetDelayedBlockingQueue<InvalidationQueueEntry> _queue;
@@ -118,6 +123,7 @@ public class InvalidationQueueService {
                    String stats = "Sent invalidation: ";
                    long success = 0;

+                    // Don't try to send same object in multiple threads
                    List<AutoCloseableNoThrow> locks = new LinkedList<>();
                    try {
                        ArrayListValuedHashMap<PeerId, Op> ops = new ArrayListValuedHashMap<>();
@@ -194,6 +200,11 @@ public class InvalidationQueueService {
        Log.info("Invalidation sender exiting");
    }

+    /**
+     * Extract operations from an object for all peers and push them.
+     *
+     * @param key the object key to process
+     */
    public void pushInvalidationToAll(JObjectKey key) {
        while (true) {
            var queue = _toAllQueue.get();
@@ -209,6 +220,7 @@ public class InvalidationQueueService {
        }
    }

+
    void pushInvalidationToOne(InvalidationQueueEntry entry) {
        if (reachablePeerManager.isReachable(entry.peer()))
            _queue.add(entry);
@@ -223,11 +235,23 @@ public class InvalidationQueueService {
            deferredInvalidationQueueService.defer(entry);
    }

+    /**
+     * Extract operations from an object for some specific peer and push them.
+     *
+     * @param host the host to extract operations for
+     * @param obj  the object key to process
+     */
    public void pushInvalidationToOne(PeerId host, JObjectKey obj) {
        var entry = new InvalidationQueueEntry(host, obj);
        pushInvalidationToOne(entry);
    }

+    /**
+     * Extract operations from an object for some specific peer and push them, without delay.
+     *
+     * @param host the host to extract operations for
+     * @param obj  the object key to process
+     */
    public void pushInvalidationToOneNoDelay(PeerId host, JObjectKey obj) {
        var entry = new InvalidationQueueEntry(host, obj);
        pushInvalidationToOneNoDelay(entry);
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
Stepan Usatiuk	c1dfe88164	quarkus update	2025-10-12 10:54:00 +02:00
Stepan Usatiuk	acf2ae2cef	less commitSnapshots created	2025-08-22 23:19:39 +02:00
Stepan Usatiuk	19016d5e46	less bad read cache	2025-08-22 18:47:43 +02:00
Stepan Usatiuk	c4945e7354	more fuse logs	2025-07-19 14:26:27 +02:00
Stepan Usatiuk	60ffc12c61	disable lazyfs tests by default still some fuse issues there	2025-06-25 18:50:19 +02:00
Stepan Usatiuk	e3e62467e4	cleanup data path config	2025-06-25 18:02:20 +02:00
Stepan Usatiuk	2434b0464f	fit.cvut.cz link fix	2025-06-12 09:52:24 +02:00
Stepan Usatiuk	ab4e06177e	add a notice	2025-06-12 09:49:30 +02:00
Stepan Usatiuk	86f240f439	cleanup dependencies a little	2025-05-14 21:45:20 +02:00
Stepan Usatiuk	59447aa286	fix windows map size	2025-05-14 20:54:59 +02:00
Stepan Usatiuk	98b7fe81ae	another note	2025-05-14 20:43:32 +02:00
Stepan Usatiuk	0713d20d95	windows note 2	2025-05-14 20:39:14 +02:00
Stepan Usatiuk	13390ba301	windows note	2025-05-14 20:24:42 +02:00
Stepan Usatiuk	b040c64da7	grammar fix	2025-05-14 20:21:19 +02:00
Stepan Usatiuk	fa9b77dc34	update java version	2025-05-14 20:20:53 +02:00
Stepan Usatiuk	508df91c0a	readme fixie	2025-05-14 19:54:31 +02:00
Stepan Usatiuk	20eb436c4b	remove readme trailing space space	2025-05-14 19:53:19 +02:00
Stepan Usatiuk	59d5b22266	improve readme 2	2025-05-14 19:52:19 +02:00
Stepan Usatiuk	4167f661e8	copy readme to run wrapper	2025-05-14 19:49:28 +02:00
Stepan Usatiuk	2cc5a703ef	Improve readme	2025-05-14 19:48:38 +02:00
Stepan Usatiuk	a5490047b8	Slight fixes	2025-05-14 19:21:00 +02:00
Stepan Usatiuk	2cd210dfd1	Slight test cleanup	2025-05-14 19:16:22 +02:00
Stepan Usatiuk	6e37c26845	Slight config cleanup	2025-05-14 19:00:51 +02:00
Stepan Usatiuk	4f7c7927f3	JAVA_HOME in run wrapper	2025-05-14 18:33:27 +02:00
Stepan Usatiuk	723a94ce0e	update readme	2025-05-14 18:11:53 +02:00
Stepan Usatiuk	57b57397b6	Dhfs-fuse: remove TieredStopAtLevel from test	2025-05-14 18:05:25 +02:00
Stepan Usatiuk	2a6656cd1a	Sync-base: increase default getSelfInfo timeout	2025-05-14 18:04:50 +02:00
Stepan Usatiuk	de5338a813	more cleanup	2025-05-14 16:52:45 +02:00
Stepan Usatiuk	8b4430fa73	Some config cleanup	2025-05-14 14:16:06 +02:00
Stepan Usatiuk	1025e6b246	Sync-base: cleanup proto files	2025-05-14 12:14:38 +02:00
Stepan Usatiuk	7274131052	update readme	2025-05-14 12:05:13 +02:00
Stepan Usatiuk	930eb38b9b	Objects: cleanup ReadTrackingSourceWrapper	2025-05-14 11:41:11 +02:00
Stepan Usatiuk	afb6f0c270	Dhfs-fuse: fix ctime	2025-05-14 11:39:40 +02:00
Stepan Usatiuk	e7f5be689f	Dhfs-fuse: report real filesystem space	2025-05-14 11:32:00 +02:00
Stepan Usatiuk	84b1d57125	Sync-base: skip scheduled execution when app is not running	2025-05-14 11:27:39 +02:00
Stepan Usatiuk	2206c13466	More lmdb logs	2025-05-14 11:18:05 +02:00
Stepan Usatiuk	d1df6b705f	Show logs for test containers that failed starting it just... doesn't start sometimes???	2025-05-14 10:38:55 +02:00
Stepan Usatiuk	83ceefa041	Sync-base: more javadocs 2	2025-05-13 23:46:07 +02:00
Stepan Usatiuk	838405fb46	Sync-base: more javadocs	2025-05-13 22:20:13 +02:00
Stepan Usatiuk	dbad8a2b22	Objects: javadocs	2025-05-13 20:53:44 +02:00
Stepan Usatiuk	66dabdef25	a couple more javadocs	2025-05-13 20:13:28 +02:00
Stepan Usatiuk	87e127bdfb	KleppmannTree javadocs and some more	2025-05-13 15:55:33 +02:00
Stepan Usatiuk	fd62543687	CI: reenable rest of CI	2025-05-12 16:15:51 +02:00
Stepan Usatiuk	757a0bbc8a	javadocs github pages (#7 ) * javadocs github pages * fix * fix * proper pages	2025-05-12 16:13:42 +02:00