Tree explorer flattening becomes inconsistent after staging/unstaging nested entries

[richardgill]

Summary

When view_mode = "tree" and flatten_dirs = true, staging or unstaging nested entries with s causes the explorer to rebuild the same path with a different flattened shape across groups.

Reproduction

1. Create a repo with modified files in nested paths, for example:
   • src/alpha/one/a.txt
   • src/alpha/one/b.txt
   • src/alpha/two/c.txt
   • src/beta/gamma/d.txt
   • docs/guide/readme.md
2. Open :CodeDiff with tree view enabled.
3. In Changes, move to src/alpha/one and press s.
4. Observe the explorer.
5. In Staged Changes, move to src/alpha/one and press s again.

Actual

After staging, the same directory hierarchy is flattened differently across groups. For example:

• Changes shows src with alpha/two under it
• Staged Changes shows src/alpha/one as a single flattened top-level node

The hierarchy jumps as files move between Changes and Staged Changes.

Expected

The explorer tree should keep a stable directory shape when entries move between groups.

I put together an AI-generated fix here: #328

Environment

• codediff.nvim commit: 93cd80c56f71af4671388c568a37d4c84c3ddefa
• Neovim: v0.11.4