fix: encoded paths are not read back

[Pfeil]

Fixes #320

The issue is actually that IDs get encoded, and their files get the encoded filenames. When reading the IDs back and decoding them, the path is not correct any more.

The fix will be:

• Filenames should use the decoded id as file name, not the encoded one
  • The fix was within a writer strategy. Ensure the other writers also do it correctly.

In order to not break existing crates:

• Reading a crate, it will detect both, files with the decoded or, as a fallback, the encoded names. This fix was in the CrateReader and applies to all strategies (folder, zip, ...).
• Saving the crate, it ensures the files are named correctly. This means affected crates can be simply read and saved again.

Other:

• Figure out what the issue of windows is, again.

Summary by CodeRabbit

• Bug Fixes

  • Improved handling of file entities whose IDs contain emojis, spaces, or other special characters.
  • Ensured encoded and decoded filenames are resolved correctly when reading crates.
  • Preserved accurate file paths for data entities after writing and reading crates.

• Tests

  • Expanded coverage for special-character IDs and encoded filenames.
  • Added validation for resolved entity paths and filename handling.

[coderabbitai]

📝 Walkthrough

Walkthrough

ReadAndWriteTest is reformatted and expanded with tests covering special-character entity identifiers, encoded filenames, decoded filenames, and resolved file paths after crate write/read operations.

Changes

Encoded path test coverage

Layer / File(s)	Summary
Path resolution coverage src/test/java/.../ReadAndWriteTest.java	Existing read/write assertions are reformatted, while new tests verify non-null paths for special-character identifiers and correct entity and filename resolution for encoded and decoded filenames.

Estimated code review effort: 2 (Simple) | ~10 minutes

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly matches the main change: fixing how encoded paths are read back from crates.

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch 320-encoded-paths-are-not-read-back-in

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[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@src/test/java/edu/kit/datamanager/ro_crate/crate/ReadAndWriteTest.java`:
- Around line 79-140: Update the folder writer to create decoded filenames, and
update the reader’s checkFolderHasFile flow to probe the decoded name first,
then the raw encoded name while preserving the directory-containment guard.
Extend testEncodedIdsFindTheirPaths to include a legacy encoded filename, then
re-save and re-read it to verify migration compatibility.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 04156f2f-d11c-411c-b9f6-69c95acef06f

📥 Commits

Reviewing files that changed from the base of the PR and between 2f83a33 and 20052d3.

📒 Files selected for processing (1)

• src/test/java/edu/kit/datamanager/ro_crate/crate/ReadAndWriteTest.java