Make setup safely refresh the runtime

[Kristof Roomp (mcroomp)]

Summary

• stop a running daemon and wait for its process lock before synchronizing .client-venv
• remove incomplete legacy .dist-info metadata that lacks RECORD
• use uv copy mode to avoid cross-filesystem hardlink warnings
• clean extension build output and exclude local/stale files from the VSIX

Validation

• ran node setup.mjs against an environment containing stale tantivy-0.26.0.dist-info; setup removed it and synchronized without warnings
• started a real daemon, reran setup, observed Shutdown sent, and confirmed the daemon was offline afterward
• extension compile succeeded
• extension tests: 68 passed, 8 integration tests skipped because the daemon was not running
• VSIX package succeeded with only the expected 14 files
• node --check setup.mjs
• git diff --check

Follow-up to #75.