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

Current Behavior

npm query ':root > *' --install-strategy=linked returns incorrect results:

1. Transitive dependencies appear as direct children of root (e.g. abbrev which is only a dependency of nopt, not a root dependency).
2. Bare store directory nodes without a name appear in results (e.g. node_modules/.store/nopt@7.2.1-... with no name field).
3. The total number of results is higher than the actual number of direct dependencies.

This affects both workspace and non-workspace projects. With the hoisted strategy, :root > * correctly returns only direct dependencies.

Expected Behavior

npm query ':root > *' should return only the direct dependencies declared in package.json. For the example below with nopt, ini, and semver as direct deps, it should return exactly 3 entries.

Steps To Reproduce

1. Create a project:

mkdir test-query && cd test-query

cat > package.json << 'EOF'
{
  "name": "test-query",
  "version": "1.0.0",
  "dependencies": { "nopt": "^7.0.0", "ini": "^4.0.0" },
  "devDependencies": { "semver": "^7.0.0" }
}
EOF

2. Install and query:

npm install --install-strategy=linked
npm query ':root > *' --install-strategy=linked

3. Returns 5 entries instead of 3. Extracting name and location:

name=abbrev, location=node_modules/.store/abbrev@2.0.0-.../node_modules/abbrev
name=ini, location=node_modules/.store/ini@4.1.3-.../node_modules/ini
name=?, location=node_modules/.store/nopt@7.2.1-...
name=semver, location=node_modules/.store/semver@7.7.4-.../node_modules/semver
name=nopt, location=node_modules/.store/nopt@7.2.1-.../node_modules/nopt

• abbrev is a transitive dep of nopt, not a root dep — should not appear.
• The entry at node_modules/.store/nopt@7.2.1-... has no name — this is a bare store directory node leaking into results.

Environment

• npm: 11.11.0
• Node.js: v22.20.0
• OS Name: macOS (Darwin 25.3.0)
• System Model Name: Mac
• npm config:

install-strategy=linked