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Closes #458. Ports upstream's [`pruneGlobalVirtualStore`](https://github.com/pnpm/pnpm/blob/94240bc046/store/controller/src/storeController/pruneGlobalVirtualStore.ts) and the read half of [`projectRegistry`](https://github.com/pnpm/pnpm/blob/94240bc046/store/controller/src/storeController/projectRegistry.ts#L37-L100) (pacquet shipped only the write half in #432 / #444). The CLI wiring already existed — `StoreCommand::Prune` → `StoreDir::prune()` — but `StoreDir::prune` was a `todo!()`. With this PR `pacquet store prune` actually runs. ## What it does **Mark phase**: walk every registered project (`<store>/projects/<short-hash>` → project root). For each project, find every `node_modules/`, follow symlinks that land under `<store>/links/...`, record reachable `<scope>/<name>/<version>/<hash>` slots, and recurse into the slot's own `node_modules/` for transitive deps. **Sweep phase**: walk `<store>/links/<scope>/<name>/<version>/<hash>` and remove every `<hash>` not in the reachable set. Empty `<version>/`, `<name>/`, and `<scope>/` parents get cleaned up. **Self-healing registry**: `get_registered_projects` unlinks entries whose project directory has been deleted (`ENOENT` on stat). Permission / unrelated errors surface as `PROJECT_INACCESSIBLE` / `PROJECT_REGISTRY_ENTRY_INACCESSIBLE` — matches upstream's strict stance, since silently dropping an inaccessible registry entry could remove slots the project still references.