[BUG] install-strategy=linked re-creates a removed workspace's directory on npm install #9331

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

While trying to fix #5463 via #9330 I found this issue

Current Behavior

When a workspace's directory has been deleted from disk and the entry has been removed from the root package.json's workspaces array, running npm install --install-strategy=linked re-creates the deleted workspace directory as an empty shell containing a self-referential symlink:

packages/b/
└── node_modules/
    └── b -> ..

No source files (no package.json, no index.js) are restored — just the directory and a <workspace>/node_modules/<name> -> .. symlink loop. The symlink target (..) points at the empty packages/b/ directory itself, so resolving it leads back to the same empty shell.

The hoisted (default) strategy does not exhibit this — the deleted directory stays deleted.

Expected Behavior

A workspace removed from package.json's workspaces array and deleted from disk should remain absent after npm install, regardless of install-strategy. The linked strategy should match the hoisted strategy's behavior here.

Steps To Reproduce

PROJ=/Users/me/tmp-cli-test  # any non-/tmp path; /tmp is /private/tmp via symlink and confuses npm
rm -rf "$PROJ" && mkdir -p "$PROJ/packages/a" "$PROJ/packages/b" && cd "$PROJ"

cat > .npmrc << 'EOF'
install-strategy=linked
EOF

cat > package.json << 'EOF'
{ "name": "host", "version": "1.0.0", "workspaces": ["packages/a", "packages/b"] }
EOF
echo '{ "name": "a", "version": "1.0.0" }' > packages/a/package.json
echo '{ "name": "b", "version": "1.0.0" }' > packages/b/package.json

npm install >/dev/null

# Remove workspace b: drop the directory AND the entry in package.json
rm -rf packages/b
node -e "const p=require('./package.json');p.workspaces=['packages/a'];require('fs').writeFileSync('./package.json',JSON.stringify(p,null,2))"

test -d packages/b && echo "before reinstall: present" || echo "before reinstall: gone"
npm install >/dev/null
test -d packages/b && echo "after reinstall:  present" || echo "after reinstall:  gone"

# Inspect what got recreated
find packages/b
readlink packages/b/node_modules/b

Observed

before reinstall: gone
after reinstall:  present
packages/b
packages/b/node_modules
packages/b/node_modules/b
..                          # ← packages/b/node_modules/b -> ..

The recreated directory contains only a self-loop symlink. There is no packages/b/package.json and no source files.

Comparison: hoisted strategy

Repeating the same steps without install-strategy=linked (or with install-strategy=hoisted) yields:

before reinstall: gone
after reinstall:  gone

Environment

• npm: built from npm/cli branch fix/prune-removed-workspace-from-package-lock at commit ea023dd0f
• Node.js: v24.15.0
• OS: macOS (Darwin 25.4.0)
• npm config:

install-strategy=linked