[BUG] `packageExtensions`-created dependencies are hidden from actual-tree commands under `install-strategy=linked`

[manzoorwanijk]

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

Under install-strategy=linked, a root packageExtensions rule adds the missing edge, the install succeeds, and the lockfile records it with packageExtensionsApplied. But every command that reads the actual installed tree loses that edge:

• npm ls --all --json omits the extension-created dependency and its provenance.
• npm explain <dep> → No dependencies found matching <dep>.
• npm patch add <dep> → EPATCHNOTINSTALLED.

Hoisted is unaffected, and normally-declared transitive deps under linked are unaffected — only edges that exist solely because of packageExtensions.

Expected Behavior

npm ls, npm explain, and npm patch add should agree with the lockfile and runtime layout under linked, as they do under hoisted.

Steps To Reproduce

broken-runtime requires missing-runtime at runtime but doesn't declare it; packageExtensions adds the edge. Use any registry serving both packages (e.g. a local one).

mkdir app && cd app
cat > .npmrc <<'EOF'
install-strategy=linked
EOF
cat > package.json <<'EOF'
{
  "name": "repro",
  "version": "1.0.0",
  "dependencies": { "broken-runtime": "1.0.0" },
  "packageExtensions": {
    "broken-runtime@1": { "dependencies": { "missing-runtime": "^1.0.0" } }
  }
}
EOF

npm install --ignore-scripts
node -e "require('broken-runtime')()"   # works at runtime

npm ls --all --json           # omits missing-runtime + packageExtensionsApplied
npm explain missing-runtime   # npm error No dependencies found matching missing-runtime
npm patch add missing-runtime # npm error code EPATCHNOTINSTALLED

# Control: drop install-strategy=linked, reinstall -> all three succeed.

Environment

• npm: 12.0.0-pre.0
• Node.js: v24.15.0
• OS: Darwin 25.5.0 (macOS, arm64)
• Config: install-strategy=linked, root packageExtensions