fix(git): complete ref update after fetch for both bare and normal repositories

[erka]

The Fetch method was not persisting fetched references to refs/heads after pulling from the remote. When using depth=1 (shallow fetches), the shallow boundary wasn't maintained and refs/heads/ were never created. For normal repos with full history, updatedRefs were collected but never written to storage.

• For shallow repositories: Create refs/heads/ and maintain shallow boundary
• For normal repositories: Create refs/heads/ from updatedRefs
• Ensure both code paths properly persist fetched references to local storage

[dosubot[bot]]

Related Documentation

1 document(s) may need updating based on files changed in this PR:

flipt

• Local Storage Git Repository Initialization

^{How did I do? Any feedback?}  

[codecov[bot]]

Codecov Report

:x: Patch coverage is 70.00000% with 12 lines in your changes missing coverage. Please review. :white_check_mark: Project coverage is 60.59%. Comparing base (2b0f8ce) to head (2c741f1).

Files with missing lines	Patch %	Lines
internal/storage/git/repository.go	70.00%	7 Missing and 5 partials :warning:

Additional details and impacted files

@@            Coverage Diff             @@
##               v2    #5144      +/-   ##
==========================================
+ Coverage   60.53%   60.59%   +0.06%     
==========================================
  Files         138      138              
  Lines       13504    13542      +38     
==========================================
+ Hits         8174     8206      +32     
- Misses       4641     4643       +2     
- Partials      689      693       +4     

Flag	Coverage Δ
integrationtests	34.77% <50.00%> (+0.09%)	:arrow_up:
unittests	51.96% <70.00%> (+0.14%)	:arrow_up:

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