pk-doctor: commands_consistency.agent-only-command fires for skills upstream doesn't ship canonical commands/ for

[projectious]

Summary

`pk-doctor`'s `commands_consistency` check emits ERROR `agent-only-command` for every `.agents/skills//SKILL.md` lacking a canonical `context/skills//commands/.md` — but upstream processkit v0.27.1 itself doesn't ship those canonical files for several skills.

Findings on ai-market-research (just upgraded to v0.27.1)

```
ERROR commands_consistency.agent-only-command
.agents/skills/pk-publish/SKILL.md
.agents/skills/pk-release/SKILL.md
.agents/skills/pk-repo-reconcile/SKILL.md
.agents/skills/pk-research/SKILL.md
.agents/skills/pk-supply-chain/SKILL.md
```

Inspecting the v0.27.1 template tree:

```bash
$ ls context/templates/processkit/v0.27.1/context/skills/processkit/release-semver/commands/ 2>&1

No such file or directory

$ ls context/templates/processkit/v0.27.1/context/skills/processkit/repo-management/commands/ 2>&1

No such file or directory

$ ls context/templates/processkit/v0.27.1/context/skills/processkit/research-with-confidence/commands/ 2>&1

No such file or directory

$ ls context/templates/processkit/v0.27.1/context/skills/processkit/supply-chain-audit/commands/
pk-supply-chain.md # <-- ONLY this one ships
```

So derived projects cannot resolve 4 of the 5 errors locally — the canonical files don't exist upstream to copy. And the pk-supply-chain one shouldn't be firing at all (the canonical `commands/pk-supply-chain.md` IS present after applying the v0.27.1 migration), so the check's matching logic may also have a bug.

Expected

Either:

1. Ship canonical `commands/.md` files for release-semver, repo-management, research-with-confidence in upstream processkit v0.27.x.
2. Allow `.agents/skills//SKILL.md` as the canonical home when no `context/skills` counterpart exists, and downgrade this check to INFO.

Plus: investigate why pk-supply-chain still fires when its canonical `commands/pk-supply-chain.md` exists.

Impact

5 ERROR findings unresolvable from derived projects — prevents `pk-doctor` from going green.