Remove deleted files as a part of the git sync path

[shangyian]

Summary

With this PR, deactivating nodes and then clicking "Sync to Git" now actually removes the stale YAMLs from the branch, rather than leaving orphans behind or 422-ing on empty namespaces.

The changes include:

• sync_namespace_to_git now detects orphan YAMLs in the existing git tree (paths under git_path that don't correspond to any active node in the namespace (e.g. deactivated nodes), and includes them as deletions in the same commit. dj.yaml is filtered out so it's never deleted.
• Removes the early 422 "namespace has no nodes to sync" error so a namespace whose nodes were all deactivated can still push the resulting deletions.
• GitHubService.commit_files accepts a deletions list, which are added to the tree as entries, which removes the path from the base tree in a single Git Data API commit.
• In the UI the success message includes a deleted N file(s) log when deletions occurred.

Test Plan

• PR has an associated issue: #
• make check passes
• make test shows 100% unit test coverage

Deployment Plan

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