fix(resolution): clear the #3500 path-resolution caches per extract() run

The memoized path/source-key lru_caches are keyed by (path, cwd) with no mtime
component; without a per-run clear they replay stale results across repeated
extract() calls in a long-lived watch/MCP process. Wire them into the existing
cache-clear block. (follow-up to #3500)