dist export leaves out tools/chemenu/tests/, tools/pytest.ini and tools/.coveragerc by exact path - the suite tests the origin repository, and 257 of its tests failed in a fresh export. dist upgrade now deletes a no-longer-shipped file that is unchanged since install, with any directory that leaves empty, and blocks one changed since install like any local change (--take-release deletes it, --keep-local keeps it). --prune is accepted and ignored. Files changed: - CHANGES.md - EVALS.md - VERSION - instructions/mcp-read-server.md - instructions/upgrade-instance.md - tools/CONTRACT.md - tools/README.md - tools/chemenu/commands/dist_cmd.py - tools/chemenu/tests/test_dist_cmd.py - tools/chemenu/tests/test_dist_upgrade.py - tools/requirements-mcp.txt Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2