Fix committing deleted files

[phillebaba]

The bootstrap code makes use of some wrapper functions to commit files. It has a workaround for a go-git bug related to broken symlinks. The issue is that this workaround does not take into account deleted files and will fail if one tries to commit a deleted file. Bootstrap will not delete any committed files from git but the Terraform provider will as it tracks the file in the state. This introduces a check which skips the broken symlink test for deleted files.

[pjbgf]

go-git using the default go-billy fs has an issue around abs symlinks pointing outside the path of their soft chroot implementation.
We no longer have that issue with our own implementation of go-billy fs: https://github.com/fluxcd/pkg/tree/main/git/gogit/fs.

Based on the above, I am not sure this will be needed once #3273 is finished.
Do you mind giving it a go with the new fs to confirm whether the issues still exists with the Terraform provider?

[aryan9600]

@phillebaba i tested deleting committed files using https://github.com/fluxcd/pkg/blob/main/git/gogit/repository_client.go#L241 and its working fine, so i think this can be superseded by #3299 when it gets merged

[phillebaba]

Sounds good will close this PR then and switch when that PR gets merged.