v0.3.1

Add update/remove commands, fix flags quoting, CI node24 migration

- mojo-pkg update: re-resolves to latest satisfying versions
- mojo-pkg remove <pkg>: removes dep from manifest, re-resolves, deletes install dir
- manifest_remove_dep() in manifest.mojo; fs_rm_rf() in fs.mojo
- 11 test suites (added test-update, test-remove)
- Fix flags.mojo: remove double-quotes from -I/-L/-rpath paths (broke
  shell $FLAGS expansion — literal quotes were passed to mojo build)
- CI: actions/checkout→v6.0.2 (node24), setup-pixi→v0.9.4 (node24)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>