feat: the test suite no longer ships, and dist upgrade deletes what a release stops shipping (#113)

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

tools/requirements-mcp.txt

@@ -8,6 +8,6 @@
 #   tools/.venv/bin/pip install -r tools/requirements-mcp.txt
 #   WIKI_TRACE=0 tools/.venv/bin/python -m chemenu.mcp --transport stdio
 #
-# The tests under `chemenu/tests/test_mcp_server.py` skip without it; CI
-# installs it, so they do run.
+# The origin repository's server tests skip without it; its CI installs it,
+# so they do run.
 mcp>=2.0