Fix/copy linked files on entry transfer

[UmutAkbayin]

Closes #12267

Adds a requirements specification file files.md documenting the linked file transfer logic between BibTeX entries in JabRef.
The document captures three key scenarios for when linked files are reachable or not in the target context and the expected behavior regarding path adjustment and file copying.

This improves traceability by formally specifying requirements that are linked to implementation and tests via OpenFastTrace.

Steps to test

• Verify that the new requirements specification file docs/requirements/files.md is present, properly formatted, and follows JabRef conventions.

• Run all existing and new unit tests in LinkedFileTransferHelperTest to ensure the linked file transfer logic behaves correctly across all covered scenarios.

• Manually verify the business logic in JabRef, especially for the scenario where the linked file is not reachable and a nested directory structure must be created. Reviewers should confirm that the path adjustments and file copying behavior conform to the requirements.

• Provide feedback if the handling of the last case (unreachable file with differing paths) aligns with project expectations.

Mandatory checks

• I own the copyright of the code submitted and I license it under the MIT license
• [.] Change in CHANGELOG.md described in a way that is understandable for the average user (if change is visible to the user)
• Tests created for changes (if applicable)
• Manually tested changed features in running JabRef (always required)
• [.] Screenshots added in PR description (if change is visible to the user)
• [.] Checked developer's documentation: Is the information available and up to date? If not, I outlined it in this pull request.
• [.] Checked documentation: Is the information available and up to date? If not, I created an issue at https://github.com/JabRef/user-documentation/issues or, even better, I submitted a pull request to the documentation repository.

[jabref-machine]

You ticked that you modified CHANGELOG.md, but no new entry was found there.

If you made changes that are visible to the user, please add a brief description along with the issue number to the CHANGELOG.md file. If you did not, please replace the cross ([x]) by a slash ([/]) to indicate that no CHANGELOG.md entry is necessary. More details can be found in our Developer Documentation about the changelog.

[trag-bot]

Using constructor for HashSet instead of modern Java collection factory method Set.of(). Modern Java practices recommend using factory methods for cleaner and more maintainable code.

[UmutAkbayin]

could not find a quick solution. would have to refactor the logic then.

[trag-bot]

Using ArrayList constructor instead of modern Java collection factory methods. Should use List.of() for empty list initialization following JabRef's conventions.

[UmutAkbayin]

could not find a quick solution. would have to refactor the logic then.

[koppor]

TracBot is wrong here 😅

[jabref-machine]

JUnit tests of jablib are failing. You can see which checks are failing by locating the box "Some checks were not successful" on the pull request page. To see the test output, locate "Tests / Unit tests (pull_request)" and click on it.

You can then run these tests in IntelliJ to reproduce the failing tests locally. We offer a quick test running howto in the section Final build system checks in our setup guide.