• Adds comprehensive guide for managing dependencies in JabRef
• Documents Java Module System (JPMS) dependency declarations
• Explains test-only dependencies and whitebox testing setup
• Covers 3rd party module versioning and patching procedures

Comprehensive dependency management documentation

• New documentation file explaining how to add and modify dependencies in JabRef
• Covers JPMS module dependencies using requires statements in module-info.java
• Documents test-only dependencies configuration in build.gradle.kts for whitebox testing
• Explains 3rd party dependency versioning through the Gradle platform in
 versions/build.gradle.kts
• Details patching procedures for non-JPMS compatible libraries using Gradle plugins

docs/code-howtos/dependency-management.md

Description

The new doc links to source files using repo-root relative paths (e.g., ../../jabgui/...), which
will be broken on the published developer documentation site because the site is built/served from
the docs/ directory only. Readers won’t be able to navigate to the referenced code/build files
from the rendered docs.

Code

docs/code-howtos/dependency-management.md[R8-13]

+With the _Java Module System (JPMS)_, dependencies between modules are
+defined in the [src/main/java/module-info.java](../../jabgui/src/main/java/module-info.java) file
+that each module contains. A dependency to another module is defined by a `requires` statement and the other module
+is identified by its _Module Name_ there. For example, a dependency to the
+[jablib](../../jablib/src/main/java/module-info.java) module is expressed by `requires org.jabref.jablib`.
+A dependency to the 3rd party library `tools.jackson.databind` is expressed by `requires tools.jackson.databind`.

Evidence

The new page contains multiple ../..//... links pointing outside docs/. The docs site build
context copies only the docs directory into the Jekyll container, so jabgui/, jablib/,
versions/, build-logic/ are not present at those relative URLs on the rendered site. Existing
docs pages typically link to source using GitHub blob/tree URLs, which work from the rendered
site.

docs/code-howtos/dependency-management.md[8-13]
docs/code-howtos/dependency-management.md[23-34]
docs/code-howtos/dependency-management.md[44-58]
docs/Dockerfile[9-14]
docs/_config.yml[27-32]
docs/code-howtos/http-server.md[7-12]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
`docs/code-howtos/dependency-management.md` links to files outside the `docs/` directory using `../../...` relative paths. Because the developer docs site is built from `docs/` only, these links will be broken for readers.
### Issue Context
Other pages in `docs/code-howtos/` typically link to source using `https://github.com/JabRef/jabref/blob/main/...` or `.../tree/main/...`.
### Fix Focus Areas
- docs/code-howtos/dependency-management.md[8-13]
- docs/code-howtos/dependency-management.md[23-34]
- docs/code-howtos/dependency-management.md[44-58]
### Suggested change
Convert each `../../<path>` link to the equivalent GitHub link, for example:
- `../../jabgui/src/main/java/module-info.java` -> `https://github.com/JabRef/jabref/blob/main/jabgui/src/main/java/module-info.java`
- `../../jabgui/src/test/java` -> `https://github.com/JabRef/jabref/tree/main/jabgui/src/test/java`
- `../../build-logic/src/main/kotlin/org.jabref.gradle.base.dependency-rules.gradle.kts` -> `https://github.com/JabRef/jabref/blob/main/build-logic/src/main/kotlin/org.jabref.gradle.base.dependency-rules.gradle.kts`

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

Description

The documentation contains a grammar error (analysis used as a verb), which reduces
professionalism and clarity for users following the dependency process. This violates the
requirement that user-facing text be typo-free and grammatically correct.

Code

docs/code-howtos/dependency-management.md[R17-18]

+Then execute `./gradlew checkAllModuleInfo` which runs a _dependency scope check_ that analysis the code to determine
+which Java types are visible (and should be visible) to which modules. If the check fails, it will advise you how to

Evidence

PR Compliance ID 25 requires user-facing text to be typo-free and grammatically correct; the added
sentence uses analysis instead of the correct verb form analyzes.

docs/code-howtos/dependency-management.md[17-18]
Best Practice: Learned patterns

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
The documentation sentence uses `analysis` incorrectly as a verb (should be `analyzes`), reducing clarity and professionalism.
## Issue Context
This is user-facing documentation about dependency management.
## Fix Focus Areas
- docs/code-howtos/dependency-management.md[17-18]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

Description

The documentation is missing an article in treat tests as separate module, which is grammatically
incorrect and may confuse readers. This violates the requirement that user-facing text be
grammatically correct.

Code

docs/code-howtos/dependency-management.md[28]

+However, it is not possible to treat tests as separate module if they break the encapsulation of the _main_ module.

Evidence

PR Compliance ID 25 requires grammatically correct user-facing text; the added line is missing an
article (a) before separate module.

docs/code-howtos/dependency-management.md[28-28]
Best Practice: Learned patterns

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
A grammar error exists in the docs: `treat tests as separate module` is missing an article.
## Issue Context
This is user-facing documentation.
## Fix Focus Areas
- docs/code-howtos/dependency-management.md[28-28]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

Description

The documentation contains a typo (lke instead of like), which reduces professionalism and can
distract readers. This violates the requirement that user-facing text be typo-free.

Code

docs/code-howtos/dependency-management.md[43]

+If you use a 3rd party module lke `tools.jackson.databind`, a version for that module needs to

Evidence

PR Compliance ID 25 requires typo-free user-facing text; the added line contains lke which is a
misspelling of like.

docs/code-howtos/dependency-management.md[43-43]
Best Practice: Learned patterns

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
A typo exists in user-facing documentation: `lke` should be `like`.
## Issue Context
This is in the dependency management how-to documentation.
## Fix Focus Areas
- docs/code-howtos/dependency-management.md[43-43]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools