In continuation of our exploration of using install-strategy=linked in the Gutenberg monorepo, which powers the WordPress Block Editor.

Under install-strategy=linked, npm query ':root > *' reported a direct dependency at its node_modules/.store/<key>/node_modules/<pkg> backing path instead of the logical node_modules/<pkg> location, diverging from the hoisted strategy.

There are two root causes.
In hasParent (query-selector-all.js), a store-backing node is isTop, has resolveParent === root, and has a top-level symlink whose parent is root, so it matched as a direct child of root through the linksIn logical-parent block that exists for workspaces.
This returned the store node alongside its logical Link.
In the query command, QuerySelectorItem read node.target.location, which for a linked dep resolves to the store node.

The fix skips store-backing nodes in the linksIn parent check, so a store node is reached only through its logical Link (matched via the edgesIn branch) rather than as a direct child of root.
The query command now reports the node's own logical location/path when the target is in the store, while workspaces and regular nodes keep the target location (for example packages/<ws>).
Deduplication now keys on the target's physical location and ranks competing representations of the same package, so a top-level placement wins over the canonical store node, which wins over an internal store symlink.
This keeps direct deps logical and transitive deps at their canonical store key for selectors such as :root *, and leaves the hoisted strategy unchanged.

References

Fixes #9617