Prepare for next major release by merging develop (5.3.0-SNAPSHOT) into the main branch (#5636)

Author: hmottestad

.github/workflows/develop-status.yml

@@ -29,7 +29,7 @@ jobs:
     - name: Build
       run: mvn -B -U clean install -Pquick,\!formatting
     - name: Verify
-      run: mvn -B install -P-skipSlowTests -Dmaven.javadoc.skip=true
+      run: ./scripts/ci/run-with-thread-dump.sh mvn -B install -P-skipSlowTests -Dmaven.javadoc.skip=true
     - name: Publish Test Report
       if: failure()
       uses: scacap/action-surefire-report@v1

.github/workflows/main-status.yml

@@ -29,7 +29,7 @@ jobs:
     - name: Build
       run: mvn -B -U -T 2C clean install -DskipTests
     - name: Run all tests
-      run: mvn -B install -P-skipSlowTests -Dmaven.javadoc.skip=true
+      run: ./scripts/ci/run-with-thread-dump.sh mvn -B install -P-skipSlowTests -Dmaven.javadoc.skip=true
     - name: Publish Test Report
       if: failure()
       uses: scacap/action-surefire-report@v1

.github/workflows/pr-verify.yml

@@ -62,7 +62,7 @@ jobs:
       - name: Build
         run: mvn --quiet clean && mvn -B --quiet -T 2C install -Pquick
       - name: Test
-        run: mvn -B test -DskipITs -P-formatting -Dmaven.javadoc.skip -Djapicmp.skip -Denforcer.skip -Danimal.sniffer.skip
+        run: ./scripts/ci/run-with-thread-dump.sh mvn -B test -DskipITs -P-formatting -Dmaven.javadoc.skip -Djapicmp.skip -Denforcer.skip -Danimal.sniffer.skip
       - name: Publish Test Report
         if: failure()
         uses: scacap/action-surefire-report@v1.9.0
@@ -84,7 +84,7 @@ jobs:
       - name: Build
         run: mvn --quiet clean && mvn -B --quiet -T 2C install -Pquick
       - name: Verify
-        run: mvn -B verify -PskipUnitTests,-formatting -Dmaven.javadoc.skip -Denforcer.skip -Danimal.sniffer.skip
+        run: ./scripts/ci/run-with-thread-dump.sh mvn -B verify -PskipUnitTests,-formatting -Dmaven.javadoc.skip -Denforcer.skip -Danimal.sniffer.skip
       - name: Publish Test Report
         if: failure()
         uses: scacap/action-surefire-report@v1.9.0
@@ -105,7 +105,7 @@ jobs:
       - name: Build
         run: mvn --quiet clean && mvn -B --quiet -T 2C install -Pquick
       - name: Verify
-        run: mvn -B verify -PslowTestsOnly,-skipSlowTests,-formatting -Dmaven.javadoc.skip -Djapicmp.skip -Denforcer.skip -Danimal.sniffer.skip
+        run: ./scripts/ci/run-with-thread-dump.sh mvn -B verify -PslowTestsOnly,-skipSlowTests,-formatting -Dmaven.javadoc.skip -Djapicmp.skip -Denforcer.skip -Danimal.sniffer.skip
       - name: Publish Test Report
         if: failure()
         uses: scacap/action-surefire-report@v1.9.0
@@ -148,12 +148,11 @@ jobs:
           node-version: 18
       - name: Run end-to-end tests of RDF4J Server and Workbench
         working-directory: ./e2e
-        run: ./run.sh
+        run: ../scripts/ci/run-with-thread-dump.sh ./run.sh
 
   copyright-check:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - name: check copyright header present
         run: scripts/checkCopyrightPresent.sh
-

.gitignore

@@ -5,8 +5,6 @@
 **/.classpath
 .settings
 **/.settings
-bin
-**/bin
 **/.factorypath
 
 # Eclipse Plug-In Settings
@@ -56,3 +54,4 @@ e2e/test-results
 /tools/server/.lwjgl/
 .m2_repo/
 .serena/
+.vscode

AGENTS.md

@@ -126,48 +126,6 @@ When writing complex features or significant refactors, use an ExecPlan (as desc
 
 When writing complex features or significant refactors, use an ExecPlan (as described in PLANS.md) from design to implementation.
 
-## PIOSEE Decision Model (Adopted)
-
-Use this as a compact, repeatable loop for anything from a one‑line bug fix to a multi‑quarter program.
-
-### P — **Problem**
-
-**Goal:** State the core problem and what “good” looks like.
-**Ask:** Who’s affected? What outcome is required? What happens if we do nothing?
-**Tip:** Include measurable target(s): error rate ↓, latency p95 ↓, revenue ↑, risk ↓.
-
-### I — **Information**
-
-**Goal:** Gather only the facts needed to move.
-**Ask:** What do logs/metrics/user feedback say? What constraints (security, compliance, budget, SLA/SLO)? What assumptions must we test?
-
-### O — **Options**
-
-**Goal:** Generate viable ways forward, including “do nothing.”
-**Ask:** What are 2–4 distinct approaches (patch, redesign, buy vs. build, defer)? What risks, costs, and second‑order effects?
-**Tip:** Check guardrails: reliability, security/privacy, accessibility, performance, operability, unit economics.
-
-### S — **Select**
-
-**Goal:** Decide deliberately and document why.
-**Ask:** Which option best meets the success criteria under constraints? Who is the decision owner? What’s the fallback/abort condition?
-**Tip:** Use lightweight scoring (e.g., Impact×Confidence÷Effort) to avoid bike‑shedding.
-
-### E — **Execute**
-
-**Goal:** Ship safely and visibly.
-**Ask:** What is the smallest safe slice? How do we de‑risk (feature flag, canary, dark launch, rollback)? Who owns what?
-**Checklist:** Traces/logs/alerts; security & privacy checks; docs & changelog; incident plan if relevant.
-
-### E — **Evaluate**
-
-**Goal:** Verify outcomes and learn.
-**Ask:** Did metrics hit targets? Any regressions or side effects? What will we keep/change next loop?
-**Output:** Post‑release review (or retro), decision log entry, follow‑ups (tickets), debt captured.
-**Tip:** If outcomes miss, either **iterate** (new Options) or **reframe** (back to Problem).
-
----
-
 ### Benchmarking workflow (repository-wide)
 
 The `scripts/run-single-benchmark.sh` helper is the supported path for spot-checking performance optimisations. It builds the chosen module with the `benchmarks` profile, constrains the benchmark selection to a single `@Benchmark` method, and when `--enable-jfr` is supplied it enforces repeatable profiling defaults (no warmup, ten 10-second measurements, one fork) while clearly reporting the destination of the generated JFR recording. Lean on this script whenever you need a reproducible measurement harness.
@@ -361,6 +319,8 @@ Why this is mandatory
     * `mvn -T 1C -o -Dmaven.repo.local=.m2_repo -Pquick clean install | tail -200`
 3. **Format (Java, imports, XML)**
     * `mvn -o -Dmaven.repo.local=.m2_repo -q -T 2C formatter:format impsort:sort xml-format:xml-format`
+    * Ensure every touched Java file has the correct agent signature comment (`// Some portions generated by Codex` for Codex, `// Some portions generated by Co-Pilot` for GitHub Co-Pilot) inserted immediately below the header before formatting.
+    * Before invoking the formatter, `cd scripts && ./checkCopyrightPresent.sh` (or use `pushd/popd`) to ensure every new or edited source file still carries the required header; fix any findings before formatting.
 4. **Targeted tests (tight loops)**
     * Module: `mvn -o -Dmaven.repo.local=.m2_repo -pl <module> verify  | tail -500`
     * Class: `mvn -o -Dmaven.repo.local=.m2_repo -pl <module> -Dtest=ClassName verify  | tail -500`
@@ -464,7 +424,6 @@ When writing complex features or significant refactors, use an ExecPlan (as desc
 
 ## Working Loop
 
-* **PIOSEE first:** restate Problem, gather Information, list Options; then Select, Execute, Evaluate.
 * **Plan:** small, verifiable steps; keep one `in_progress`, or follow PLANS.md (ExecPlans)
 * **Change:** minimal, surgical edits; keep style/structure consistent.
 * **Format:** `mvn -o -Dmaven.repo.local=.m2_repo -q -T 2C formatter:format impsort:sort xml-format:xml-format`
@@ -570,6 +529,10 @@ Hint: get the current year with `date +%Y`.
 
 Do **not** modify existing headers’ years.
 
+Right below the header block, insert an agent signature comment: Codex agents must add `// Some portions generated by Codex`, and GitHub Co-Pilot agents must add `// Some portions generated by Co-Pilot`. Align the wording with whatever agent name you are currently operating under.
+
+Immediately after creating any new Java source file, add the signature comment (per rule above) and run `cd scripts && ./checkCopyrightPresent.sh` (or an equivalent pushd/popd invocation) so you catch missing copyright/SPDX lines before moving on.
+
 ---
 
 ## Pre‑Commit Checklist
@@ -651,7 +614,6 @@ Do **not** modify existing headers’ years.
 * **Files touched:** list file paths.
 * **Commands run:** key build/test commands.
 * **Verification:** which tests passed, where you checked reports.
-* **PIOSEE trace (concise):** P/I/O summary, selected option/routine, key evaluate outcomes.
 * **Evidence:**
   *Routine A:* failing output (pre‑fix) and passing output (post‑fix).
   *Routine B:* pre‑ and post‑green snippets from the **same selection** + **Hit Proof**.

assembly-descriptors/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>org.eclipse.rdf4j</groupId>
 		<artifactId>rdf4j</artifactId>
-		<version>5.2.3-SNAPSHOT</version>
+		<version>5.3.0-SNAPSHOT</version>
 	</parent>
 	<artifactId>rdf4j-assembly-descriptors</artifactId>
 	<name>RDF4J: Assembly Descriptors</name>

assembly/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>org.eclipse.rdf4j</groupId>
 		<artifactId>rdf4j</artifactId>
-		<version>5.2.3-SNAPSHOT</version>
+		<version>5.3.0-SNAPSHOT</version>
 	</parent>
 	<artifactId>rdf4j-assembly</artifactId>
 	<packaging>pom</packaging>

bom/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>org.eclipse.rdf4j</groupId>
 		<artifactId>rdf4j</artifactId>
-		<version>5.2.3-SNAPSHOT</version>
+		<version>5.3.0-SNAPSHOT</version>
 	</parent>
 	<artifactId>rdf4j-bom</artifactId>
 	<packaging>pom</packaging>

compliance/elasticsearch/pom.xml

@@ -4,21 +4,31 @@
 	<parent>
 		<groupId>org.eclipse.rdf4j</groupId>
 		<artifactId>rdf4j-compliance</artifactId>
-		<version>5.2.3-SNAPSHOT</version>
+		<version>5.3.0-SNAPSHOT</version>
 	</parent>
 	<artifactId>rdf4j-elasticsearch-compliance</artifactId>
 	<name>RDF4J: Elasticsearch Sail Tests</name>
 	<description>Tests for Elasticsearch.</description>
 	<!-- disable the Java security manager for elasticsearch tests -->
 	<build>
 		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-surefire-plugin</artifactId>
+				<configuration>
+					<systemPropertyVariables>
+						<elasticsearch.docker.version>${elasticsearch.version}</elasticsearch.docker.version>
+					</systemPropertyVariables>
+				</configuration>
+			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-failsafe-plugin</artifactId>
 				<configuration>
 					<forkCount>0</forkCount>
 					<systemPropertyVariables>
 						<tests.security.manager>false</tests.security.manager>
+						<elasticsearch.docker.version>${elasticsearch.version}</elasticsearch.docker.version>
 					</systemPropertyVariables>
 				</configuration>
 			</plugin>
@@ -37,34 +47,6 @@
 			<version>${project.version}</version>
 			<scope>test</scope>
 		</dependency>
-		<dependency>
-			<groupId>org.apache.lucene</groupId>
-			<artifactId>lucene-test-framework</artifactId>
-			<version>${lucene.version}</version>
-			<scope>test</scope>
-			<exclusions>
-				<exclusion>
-					<groupId>org.hamcrest</groupId>
-					<artifactId>hamcrest-core</artifactId>
-				</exclusion>
-			</exclusions>
-		</dependency>
-		<dependency>
-			<groupId>org.elasticsearch.test</groupId>
-			<artifactId>framework</artifactId>
-			<version>${elasticsearch.version}</version>
-			<scope>test</scope>
-			<exclusions>
-				<exclusion>
-					<groupId>commons-logging</groupId>
-					<artifactId>commons-logging</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>org.apache.httpcomponents</groupId>
-					<artifactId>httpcore</artifactId>
-				</exclusion>
-			</exclusions>
-		</dependency>
 		<dependency>
 			<groupId>org.apache.httpcomponents</groupId>
 			<artifactId>httpcore</artifactId>
@@ -105,12 +87,32 @@
 			<version>${elasticsearch.version}</version>
 			<scope>test</scope>
 			<exclusions>
+				<exclusion>
+					<groupId>commons-logging</groupId>
+					<artifactId>commons-logging</artifactId>
+				</exclusion>
 				<exclusion>
 					<groupId>com.vividsolutions</groupId>
 					<artifactId>jts</artifactId>
 				</exclusion>
+				<exclusion>
+					<groupId>org.elasticsearch</groupId>
+					<artifactId>jna</artifactId>
+				</exclusion>
 			</exclusions>
 		</dependency>
+		<dependency>
+			<groupId>org.testcontainers</groupId>
+			<artifactId>testcontainers</artifactId>
+			<version>${testcontainers.version}</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.testcontainers</groupId>
+			<artifactId>junit-jupiter</artifactId>
+			<version>${testcontainers.version}</version>
+			<scope>test</scope>
+		</dependency>
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
 			<artifactId>log4j-core</artifactId>