install: remove node_modules entries that left the lockfile - #32974

Under the isolated linker, the kept set unions `root_pkg_deps` (flag-independent) with `entry_dependencies[ROOT]`, but the latter is built by the store pass that calls `is_filtered_dependency_or_workspace` and so is narrowed by `--filter`. A `publicHoistPattern` hoist that comes from a filtered-out workspace's transitive is therefore in neither set, and `bun install --filter=...` deletes it from the root `node_modules` even though the full lockfile still places it there. The hoisted linker avoid

The prune is not gated on `!this.options.global`, so any `bun add -g <pkg>` / `bun install -g` chdirs to the global install dir and prunes `<global_dir>/node_modules`. `bun link` (no args) creates a bare symlink there without touching the global package.json/lockfile, so the linked name is never in `expected_root_entries` and gets `delete_tree`'d — every `bun link` registration (and its global bin shim, via the follow-on `prune_dangling_bin_links`) is silently destroyed by the next global instal