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

instructions/mcp-read-server.md

@@ -106,8 +106,8 @@ everything an operator needs that is *true of the software* rather than of one i
   sync is not running. If it is `null`, the served tree has uncommitted changes - something is
   writing into the corpus that should not be.
 - **The server disagrees with `wikitool` on the same query?** That is a defect, not a
-  configuration difference: the two go through the same functions and a golden test holds their
-  output together (`tools/chemenu/tests/test_mcp_server.py`). Check first that both are pointed
+  configuration difference: the two go through the same functions and a golden test in the origin
+  repository holds their output together. Check first that both are pointed
   at the same root - `CHEMENU_ROOT` is easy to set for one and not the other.
 - **Asked to expose a write tool?** Five of the six tools have none, structurally: the server
   imports nothing under `chemenu.commands`, so `new`, `touch`, `xref`, `cite`, `publish` and