Ensure only files are in file overview in config apply request

[dhurley]

Proposed changes

Ensure only files are in file overview in config apply request.

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• I have run make install-tools and have attached any dependency changes to this pull request
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[codecov]

Codecov Report

❌ Patch coverage is 80.95238% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 86.41%. Comparing base (34a13e6) to head (bea3f91).
⚠️ Report is 2 commits behind head on release-3.5.1.

Files with missing lines	Patch %	Lines
internal/file/file_manager_service.go	80.95%	2 Missing and 2 partials ⚠️

Additional details and impacted files

@@              Coverage Diff               @@
##           release-3.5.1    #1395   +/-   ##
==============================================
  Coverage          86.41%   86.41%           
==============================================
  Files                102      102           
  Lines              12585    12604   +19     
==============================================
+ Hits               10875    10892   +17     
  Misses              1233     1233           
- Partials             477      479    +2     

Files with missing lines	Coverage Δ
internal/file/file_manager_service.go	75.31% <80.95%> (+0.18%)	⬆️

... and 1 file with indirect coverage changes

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[vrmare]

I think this function can be refactored for simplicity? I imagine existing manifest (source of truth) is maintained as a virtual FS in memory. Then single loop over modified files can be applied to the VFS.

Something like this:

type VirtualFS struct {
    files map[string]SomeFileCache
    mu    sync.RWMutex
}

func (vfs *VirtualFS) ApplyChanges(modifiedFiles map[string]SomeFileCache) ([]FileAction, error) {}

The idea is that VFS holds canonical state.

[vrmare]

A bigger change I believe and happy to discuss outside this PR.

[dhurley]

Yeah we can take a look at this and do any changes in a separate PR