fix(cli): use additive merge in profile install/update to preserve local skills

[zccyman]

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

Scenario	Before	After
Install to empty profile	Works	Works (same)
Install to profile with local skills	Local skills deleted	Local skills preserved
Update distribution skill	Works	Works (overwrites only dist files)
Update with new dist skill	Works	Works (new skill added)
Nested directory merge	Broken (rmtree kills everything)	Correct (recursive additive)

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

File	Change
hermes_cli/profile_distribution.py	Add _additive_copytree helper; replace rmtree+copytree with additive merge
tests/hermes_cli/test_profile_distribution_additive.py	New: 8 tests

Closes #25120

[teknium1]

Thanks for addressing the destructive profile-update path; current main still has the rmtree(dest) behavior at hermes_cli/profile_distribution.py:573-577, so the underlying report is valid.

Problems

• The new helper applies its ignore callback at every recursive level (hermes_cli/profile_distribution.py:541-545 in this PR). The supplied callback excludes every nested basename in USER_OWNED_EXCLUDE, which regresses the nested-path fix in e53b74c39450d85d210ba06e69be5022278eb974; current regression coverage starts at tests/hermes_cli/test_profile_distribution.py:505.
• A fully additive traversal retains removed distribution files indefinitely. The documented contract says distribution-owned paths are replaced (website/docs/user-guide/profile-distributions.md:247), but the added tests do not cover a removed or renamed shipped file.

Suggested changes

• Preserve the current root-only exclusion behavior when salvaging; the outer staged-root guard already filters protected root paths.
• Add an update test for removed/renamed shipped content and implement the selected replacement policy. Linked PR #44386 contains a related selective-merge approach worth comparing.

Automated hermes-sweeper review.

[teknium1]

Forwarding this callback recursively reintroduces the nested-basename exclusion fixed on main by e53b74c: USER_OWNED_EXCLUDE entries such as tools/bin or skills/<category>/hermes-agent are skipped at every depth. Keep the current root-only exclusion behavior; the outer staged-root loop already filters protected root entries.