chore: Better temp directory cleanup in TestGenerateManifestsHelmWithRefs_CachedNoLsRemote

[andrii-korotkov-verkada]

Helps with #20035

There are occasional failures due to unlinking .git file. An improvement can be made to set permissions on directories as files as much as we can instead of stopping completely on error.

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[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 55.15%. Comparing base (b78f209) to head (4438287). Report is 21 commits behind head on master.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #20780 +/- ## ========================================== - Coverage 55.17% 55.15% -0.02% ========================================== Files 324 324 Lines 55259 55256 -3 ========================================== - Hits 30487 30475 -12 - Misses 22158 22165 +7 - Partials 2614 2616 +2 ```

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