[BUG] install-strategy=linked: Installed transitive optional dependency is not materialized in the actual tree with install-strategy=linked #9627

Part of #9608.

Scope: this affects transitive optional dependencies — ones a non-root package depends on, which under linked live as siblings in the store. A root-declared optional dependency works correctly (it is symlinked into the top-level node_modules and loaded as a direct child of the root, so it never relies on the affected code path). This is the general root cause behind the "extension-added optional dep reported UNMET" finding (sweep BUG 15); the trigger there is not the extension but that the optional dep is transitive.

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, an optional dependency that is actually installed is missing from the tree that loadActual builds. The package is present on disk — extracted into node_modules/.store, with a valid symlink into its consumer's store node_modules — yet read commands that walk the actual tree do not see it:

• npm ls reports UNMET OPTIONAL DEPENDENCY fsevents@~2.3.2, even though fsevents is installed.
• npm sbom omits the package entirely (undercounts components versus hoisted).

Hoisted produces the correct result for the same dependency set (fsevents@2.3.3 shown by ls, present in the SBOM).

This is distinct from the transitive-devDependencies ESBOMPROBLEMS bug (#9610): there the linked tree reported too many required edges; here an installed optionalDependency is reported as unmet/absent (too few).

Expected Behavior

An optional dependency that is installed in the store must appear in the actual tree under install-strategy=linked, identical to the hoisted strategy — npm ls should show it as installed (not UNMET), and npm sbom should include it.

Steps To Reproduce

cd "$(mktemp -d)"
echo 'install-strategy=linked' > .npmrc
cat > package.json <<'EOF'
{ "name": "opt", "version": "1.0.0", "dependencies": { "chokidar": "3.6.0" } }
EOF
npm install >/dev/null

# fsevents IS installed in the store:
ls node_modules/.store | grep fsevents
#   fsevents@2.3.3-...

# ...but the actual tree does not see it:
npm ls --all | grep -i fsevents
#   UNMET OPTIONAL DEPENDENCY fsevents@~2.3.2

npm sbom --sbom-format=cyclonedx | grep -c fsevents
#   0

Works with hoisted strategy (control)

rm -rf node_modules package-lock.json .npmrc
npm install --install-strategy=hoisted >/dev/null
npm ls --all | grep -i fsevents
#   fsevents@2.3.3

Environment

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

install-strategy=linked

Related: #9608, #9610.