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

EVALS.md

@@ -9,8 +9,8 @@ that [AGENTS.md](AGENTS.md) exists to prevent.
 
 ## Why, beyond the unit tests
 
-The pytest suite under `tools/chemenu/tests/` checks the **compiler**: given this input,
-does `wikitool` produce that output. It says nothing about the two things that actually go
+The pytest suite under `tools/chemenu/tests/` - in the origin repository; `dist export` does
+not ship it - checks the **compiler**: given this input, does `wikitool` produce that output. It says nothing about the two things that actually go
 wrong in practice - whether the *agent* followed the contracts, and whether the pages it wrote
 are any good.