Summary

_copy_dist_payload used shutil.rmtree + copytree for all directories, destroying locally-installed skills on every hermes profile install or hermes profile update. The distribution_owned manifest field was parsed but never enforced during the copy phase.

Before

# _copy_dist_payload — line 554-561
dest = target / name
if entry.is_dir():
    if dest.exists():
        shutil.rmtree(dest)    # ← deletes ALL local skills!
    shutil.copytree(entry, dest, ...)

Walking a profile with skills/devops/my-custom-skill/ → gone after update.

After

New _additive_copytree helper walks the source tree and copies/overwrites only files present in the distribution, preserving everything else:

def _additive_copytree(src: Path, dst: Path, ignore=None) -> None:
    if not dst.exists():
        shutil.copytree(src, dst, ignore=ignore)
        return
    for entry in src.iterdir():
        dest_entry = dst / entry.name
        if entry.is_dir():
            _additive_copytree(entry, dest_entry, ignore=ignore)  # recurse
        else:
            shutil.copy2(entry, dest_entry)  # overwrite only this file

Behavior

Testing

• 8 new tests:
  • 5 unit tests for _additive_copytree (new files, preserve local, overwrite dist, nested merge, ignore)
  • 3 integration tests for _copy_dist_payload (install preserves locals, update overwrites dist only, fresh install)
• 71 existing profile distribution tests passing (0 regressions)

Files changed

Closes #25120