[BUG] install-strategy=linked: extension-added optional dependency reported UNMET by npm ls though installed #9622

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

When a root manifest extension (packageExtensions or .npm-extension transformManifest) adds an optionalDependencies entry to a package, the optional dependency is correctly materialized under install-strategy=linked (symlinked into the consumer's store node_modules, resolves at runtime), but npm ls reports it as UNMET OPTIONAL DEPENDENCY. The hoisted strategy reports it as installed. A normal (non-extension) optional dependency reports correctly under linked, and extension-added required/peer dependencies also report correctly — only the extension + optional combination misreports.

Expected Behavior

An extension-added optional dependency that is installed should be reported as present (not UNMET) by npm ls under the linked strategy, matching the hoisted strategy.

Steps To Reproduce

cd "$(mktemp -d)"
echo 'install-strategy=linked' > .npmrc
cat > package.json <<'EOF'
{ "name": "po", "version": "1.0.0", "dependencies": { "is-odd": "3.0.1" },
  "packageExtensions": { "is-odd@3": { "optionalDependencies": { "abbrev": "^2.0.0" } } } }
EOF
npm install >/dev/null

# materialized correctly:
ls node_modules/.store/is-odd@*/node_modules/abbrev   # present (symlink)
node -e 'const p=require.resolve("is-odd"); require.resolve("abbrev",{paths:[p]}); console.log("resolves OK")'

# but npm ls misreports:
npm ls --all
#   linked:  is-odd@3.0.1 -> ... ├── UNMET OPTIONAL DEPENDENCY abbrev@^2.0.0   (incorrect)
#   hoisted: is-odd@3.0.1     ├── abbrev@2.0.0                                 (correct)

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