feat(skills): add atomic skill design and global store

[rgdevme]

What changed

• add the atomic design skill and simplify its slot helper
• reconcile skills concurrently while reporting percentage, total, reused, and fetched counters
• replace project-local skill caching with a verified user-level content-addressed store shared across repositories
• pin remote installations to the exact checked-out commit
• materialize independent project-owned skill directories through copy-on-write cloning, hard links, or copies
• migrate valid legacy caches safely and retain them when migration cannot complete
• isolate and clean repository staging under .agnos/tmp
• document the reconciliation model and global-store architectural decision

Why

Project-local repository and skill caches duplicated content across projects and could hit intermittent Windows publication failures. Linked project materializations also coupled installed skills to cache lifetime. The shared verified store provides cross-project reuse while independent project directories remain usable if the store is removed.

Impact

Locked skills can install without Git access when their content hash is already present globally. Warm installs reuse content across repositories, corrupt entries are rejected, branch movement cannot change a locked installation, and AGNOS_STORE_DIR can override the platform data location.

Validation

• pnpm lint (0 errors; 108 existing warnings)
• pnpm typecheck
• pnpm test (291 tests)
• pnpm build
• Windows smoke test in tst: second install reused 86 skills with 0 fetches, removed the legacy cache, and left 0 linked project skills

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