Add whet install --prune (manifest-scoped, safe alongside other tools' skills)

[ortizeg]

Problem

whet install copies skills but never removes ones deleted upstream. After the recent cleanup, 8 deleted skills were still installed and still being loaded by Claude Code:

code-review  data-engineer  devops-infra  dvc
expert-coder  ml-engineer  pydantic-strict  test-engineer

So the broken "agents" (the ones with no frontmatter), the removed dvc, and a stale pydantic-strict sitting next to the new pydantic were all still live. The repo was clean; the installed copies were not.

Why this isn't just rm -rf

A skills directory is shared. ~/.claude/skills/ here holds 104 skills — most of them GSD's, plus interface-design and hand-written ones. A prune that removed "anything not in whet's skills/" would delete all of them.

So prune is manifest-scoped:

• Each install writes .whet-manifest.json into the target directory, recording which skills whet owns there.
• Prune only ever removes names from that manifest → skills owned by other tools are invisible to it.
• Orphans are computed against the unfiltered source set, so a skill merely skipped by --category or by the extra tier is never mistaken for a deleted one.
• Without --prune, orphans are reported, not touched.
• A corrupt or missing manifest yields an empty owned-set, which fails safe — prune is authorized to remove nothing.

Usage

whet install --prune

Installs predating the manifest are invisible to prune by design (whet has no record it owns them); clear those once with whet remove <name>.

Tests

10 new tests in tests/test_manifest.py, including the two that matter:

• test_find_orphans_ignores_skills_whet_did_not_install — the GSD/interface-design protection
• test_find_orphans_ignores_filtered_but_existing_skills — an extra skill skipped this run is not an orphan
• plus corrupt-manifest and wrong-shape tolerance

202 passed; ruff, mypy --strict, and mkdocs build --strict clean.

🤖 Generated with Claude Code