Background

#432 landed Stage 1 of the global virtual store. Frozen-lockfile installs now write package contents to <store_dir>/links/<scope>/<name>/<version>/<hash>/node_modules/<name> and register each importer at <store_dir>/projects/<short-hash> → project root. Without a prune sweep, both directories grow unbounded — old slots and dead-project entries accumulate forever.

The "Out of scope" section of #432 flagged this as a dedicated follow-up.

What needs to happen

Port upstream's pruneGlobalVirtualStore and expose it via a pacquet store prune subcommand.

Upstream's mark-and-sweep:

1. Get registered projects: list <store_dir>/projects/, resolve each symlink target, drop entries whose target is gone. Upstream's getRegisteredProjects already has the stale-entry cleanup; pacquet only ships register_project from that file today (see crates/store-dir/src/project_registry.rs), so the read side needs porting too.
2. Mark phase: for each surviving project, find every node_modules/ directory (root + workspace packages), walk every symlink that lands under <store_dir>/links/..., record the resolved slot path in a reachable set.
3. Sweep phase: walk <store_dir>/links/<scope>/<name>/<version>/, delete any <hash> subdirectory not in the reachable set. Empty <version>/ and <name>/ parents get cleaned up in a second pass.

Today

• <store_dir>/links/... keeps growing as projects upgrade dependency versions.
• <store_dir>/projects/<hash> symlinks linger for projects the user has deleted.
• No CLI surface for either cleanup.

Plan

1. Port getRegisteredProjects (with the stale-entry cleanup) into pacquet_store_dir::project_registry.
2. Add pacquet_store_dir::prune_global_virtual_store(store_dir) that runs the mark-and-sweep.
3. Add a pacquet store prune subcommand (mirror pnpm store prune) that calls it.
4. Tests:
   • End-to-end: register two projects, delete one project's dir on disk, run prune, assert the dead project's registry entry is gone and any slots only it referenced are gone.
   • Mark phase: workspace with two node_modules/ dirs that both reference the same slot — slot is kept after either project is removed.
   • Sweep phase: orphan slot under <store_dir>/links/... with no project reference gets removed.

Out of scope

• Pacquet's per-store-version GC (the legacy non-GVS <store>/v11/files/ shards). That's a different cleanup with different lifetime semantics.

References

• Upstream: pruneGlobalVirtualStore
• Upstream: getRegisteredProjects cleanup
• pacquet today: crates/store-dir/src/project_registry.rs (the write half from Add global virtual store support to pacquet install --frozen-lockfile #432 / feat: global-virtual-store foundation (#432 partial) #444)
• Tracked from: Add global virtual store support to pacquet install --frozen-lockfile #432 (Out of scope)

Written by an agent (Claude Code, claude-opus-4-7).