fix: keep nested file: deps and re-resolve changed git refs (#9523)

The lockfile pruning added in 11.15.0 dropped every extraneous node
outside node_modules to remove stale workspace entries. This also
removed legitimate nested entries for a file: dependency that itself has
a file: dependency (e.g. lib/b/lib/a), leaving the lockfile incomplete
so `npm ci` failed with "Missing: a@1.0.0 from lock file".
 
Only prune extraneous nodes that are direct fsChildren of the root or
detached link targets (removed workspaces, removed root-level file:
deps, orphaned link targets). Extraneous fsChildren nested under another
package are kept so `npm ci` can resolve the parent's dependency.
 
Fixes: https://github.com/npm/cli/issues/9433
Fixes: https://github.com/npm/cli/issues/9486
Supersedes: https://github.com/npm/cli/pull/9524