[BUG] `install-strategy=linked`: `.store` and stale directories not cleaned up when switching install strategy

[manzoorwanijk]

Part of #9608.

Is there an existing issue for this?

• I have searched the existing issues

This issue exists in the latest npm version

• I am using the latest npm

This is not just a request to bump a dependency for a CVE

• This is not solely a request to bump a dependency for a CVE

Current Behavior

Switching the install strategy in the same project directory leaves stale state in both directions. Switching hoisted → linked leaves the previous strategy's real top-level transitive directories (e.g. balanced-match, brace-expansion, concat-map) on disk alongside the new .store/ and symlinks. Switching linked → hoisted leaves the entire node_modules/.store/ directory behind. A fresh install of either strategy produces a clean layout.

Expected Behavior

Switching strategy should remove the layout artifacts of the previous strategy: stale top-level real directories should be cleaned up when entering the linked strategy, and .store/ should be removed when leaving it.

Steps To Reproduce

cd "$(mktemp -d)"
echo '{ "name": "sw", "version": "1.0.0", "dependencies": { "minimatch": "3.0.4" } }' > package.json

echo 'install-strategy=hoisted' > .npmrc
npm install >/dev/null            # real dirs: balanced-match, brace-expansion, concat-map, minimatch
echo 'install-strategy=linked' > .npmrc
npm install >/dev/null
ls -l node_modules | grep -E 'balanced-match|brace-expansion|concat-map'  # still real dirs (stale)
# a fresh linked install has only `minimatch` (symlink) + .store/

# reverse direction:
echo 'install-strategy=hoisted' > .npmrc
npm install >/dev/null
ls node_modules/.store            # still present (stale); a fresh hoisted install has no .store

Environment

• npm: 12.0.0-pre.1 (latest)
• Node.js: v24.17.0
• OS Name: macOS (Darwin 25.5.0)
• System Model Name: MacBook (arm64)
• npm config:

install-strategy=linked