Modularize Neo4j configuration to support profile changes

[JohT]

🚀 Feature

• Modularize Neo4j configuration and support profile changes: With useNeo4jHighMemoryProfile.sh you can now switch to the new high memory profile without redoing the whole analysis. This is helpful when you reach memory limits within your first analysis attempt and want to fix that in a simple way.

⚙️ Optimization

• Improved fail-fast when running all tests.
• Support direct and sourced test runs: You can now run each test case directly without getting an error that the script needs to be sourced. The sourced run of all tests with runTests.sh is not affected and runs as usual.

🛠 Fix

• Fix temporary directory name in maven test: The test results will now be written into a properly named temporary directory.
• Fix documentation grammer issues

[Copilot]

Pull request overview

This PR modularizes Neo4j configuration into a reusable configureNeo4j.sh script, adds a helper to switch to a high-memory profile post-setup, and improves the bash test harness to support both sourced and direct execution with better fail-fast behavior.

Changes:

• Introduce scripts/configureNeo4j.sh and a useNeo4jHighMemoryProfile.sh wrapper for switching Neo4j config templates.
• Refactor setupNeo4j.sh to reuse the new configuration script.
• Adjust test runner/tests to support direct execution and improve fail-fast behavior; fix mktemp temp-dir naming in one test.

Reviewed changes

Copilot reviewed 20 out of 20 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
scripts/useNeo4jHighMemoryProfile.sh	New helper script to apply the high-memory Neo4j config template.
scripts/configureNeo4j.sh	New modular Neo4j configuration logic (templating/idempotent reconfiguration).
scripts/setupNeo4j.sh	Reuses configureNeo4j.sh instead of embedding configuration logic.
scripts/runTests.sh	Runs test scripts without piping into while to support fail-fast on exit.
scripts/testConfigureNeo4j.sh	New integration/validation tests for configureNeo4j.sh.
scripts/testInstallJavaScriptDependencies.sh	Make success path return/exit correctly when sourced vs executed.
scripts/testFilenameReferences.sh	Make success path return/exit correctly when sourced vs executed.
scripts/testDownloadMavenArtifacts.sh	Fix mktemp dir naming; make success path return/exit correctly.
scripts/testDetectChangedFiles.sh	Make success path return/exit correctly when sourced vs executed.
scripts/testCloneGitRepository.sh	Make success path return/exit correctly when sourced vs executed.
scripts/markdown/testFormatQueryResultAsMarkdownTable.sh	Make success path return/exit correctly when sourced vs executed.
scripts/markdown/testEmbedMarkdownIncludes.sh	Make success path return/exit correctly when sourced vs executed.
scripts/configuration/template-neo4j.conf	Remove template header comment (templates now appended with a generated eye-catcher).
scripts/configuration/template-neo4j-v4.conf	Remove template header comment (same rationale).
scripts/configuration/template-neo4j-v4-low-memory.conf	Remove template header comment (same rationale).
scripts/configuration/template-neo4j-low-memory.conf	Remove template header comment (same rationale).
scripts/configuration/template-neo4j-high-memory.conf	Remove template header comment (same rationale).
init.sh	Adds forwarding script creation for useNeo4jHighMemoryProfile.sh.
README.md	Documents switching to high-memory profile after setup.
COMMANDS.md	Adds manual command docs for applying a different Neo4j config template and workspace hints.

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