Fix IllegalArgumentException with duplicate natures

[laeubi]

Changed ProjectDescription.hasPrivateChanges() to use HashSet instead of Set.of() to handle duplicate natures gracefully. Set.of() throws IllegalArgumentException on duplicates, but HashSet tolerates them and correctly compares nature sets.

Also added test case testDuplicateNatures() to ensure this regression doesn't occur again.

Derived from here:

• Fix IllegalArgumentException when updating project configuration with duplicate natures #2183

[laeubi]

ECA check failure is due:

• https://gitlab.eclipse.org/eclipsefdn/helpdesk/-/issues/6562

and currently unavoidable, I plan to merge anyways if build succeeds here as it is the same solution that was suggested by @merks and its more a technical detail. If there will be ever concerns regarding AI generated content, the only new thing is the test what then can be deleted without any problem.

[github-actions]

Test Results

 1 947 files  ±0   1 947 suites  ±0   1h 33m 3s ⏱️ - 6m 45s
 4 721 tests +1   4 697 ✅ +1   24 💤 ±0  0 ❌ ±0 
14 163 runs  +3  13 996 ✅ +3  167 💤 ±0  0 ❌ ±0 

Results for commit f0dcc19. ± Comparison against base commit c1f0dd4.

[merks]

The content is simple, follows the original suggestion of mine in the issue, and the test case is mechanical in nature.