Add suite-aware skill updates and targeted native projection

[rudijetson]

Summary

• add targeted native-skill projection for exact installed RUDI skill IDs
• add suite-aware updates through Registry related.skills
• require explicit whole-inventory consent and keep dry-run, JSON, and help output truthful
• preserve partial suite results and propagate native-projection failures
• regenerate the tracked CLI bundle and document the governed verification record

Issue

Fixes #32

SWE Checklist

docs/swe-compliance/2026-08-27-delivery-loop-install-update.md

Risk

• Tier: Medium
• Rationale: Changes update orchestration, CLI argument handling, and native skill projection, but adds no dependency or persistent-schema migration.
• Rollback: Revert commits 9635387 and 7e0b73b before release. No user data migration is required.

Proof

• Red-green behavior sequence is recorded in the checklist.
• Final focused tests: 136/136 passed.
• Full suite: 689/689 passed, 0 failed.
• Repeated build was deterministic; dist/index.cjs SHA-256: 985acd742bf5fbf6c05cce0cadf8899ef68043748409d7d13e79510fe5f18cbd.
• Changed-file debt scan: status ok, 0 findings.
• npm pack --dry-run --json: passed with six intended publish entries.
• git diff --check: passed.
• Isolated temporary-home smoke covered targeted projection, suite-aware dry-run, JSON parseability, and preservation of an unrelated wrapper.

Independent Review

A fresh-context reviewer initially blocked publication on four correctness findings: boolean flags consuming exact IDs, external-native skill provenance, lost partial-suite outcomes, and projection failures returning false success. All four were reproduced with failing tests and remediated. The final independent re-review passed with no blocking finding or regression.

Accepted Debt

None.

Proof Gaps

• The modified CLI was not installed or synchronized to another Mac.
• Temporary smoke homes were intentionally retained as evidence.
• Worktree closeout and branch cleanup are deferred until separately approved.

Gate Boundary

This PR does not authorize merge, release, installation, primary-Mac synchronization, or branch/worktree cleanup.