feat: support project-scoped lockfiles and renamed skill installs

[farnoodma]

Summary

This PR implements the two CLI capabilities requested around update tracking and rename support:

• Project + global lock scope support

  • skills add now tracks installs in both scopes:
    • project: <cwd>/.agents/.skill-lock.json
    • global: ~/.agents/.skill-lock.json
  • skills check / skills update now read both scopes by default.
  • Added explicit scope flags:
    • --project / -p: project only
    • --global / -g: global only

• --rename support for installs

  • Added --rename <name> to skills add for single-skill installs.
  • Rename applies to:
    • installation folder name
    • name frontmatter in installed SKILL.md
  • Guardrail: --rename fails when multiple skills are selected.

• Rename-aware updates

  • skills update preserves local installed names by reinstalling with --rename <installed-name>.
  • This ensures skills installed from source X as local alias Y stay as Y after updates.

Implementation Notes

• Split into two commits for review clarity:
  1. feat: track and update skills in project and global scopes
  2. feat: add renamed skill installs and preserve aliases on update
• Updated docs/help text in README.md, AGENTS.md, and CLI help output.
• Added focused tests for scope parsing/behavior, lock scope behavior, and rename install behavior.

Test plan

• pnpm install --frozen-lockfile
• pnpm build
• pnpm format:check
• pnpm test
• node scripts/validate-agents.ts

[vercel]

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[farnoodma]

@quuu this PR adds project-scoped lock tracking + --rename support with full test coverage. Would appreciate your review when you have a moment.

[farnoodma]

Superseded by #369 (same changes, but commits are re-signed with my personal GPG key fa.massoudi@gmail.com).