fix: publish/sync merge generated files mechanically and carry non-overlapping uncommitted work through a rebase (#180)

Overlap only in kb/index.md, kb/log.md, kb/provenance.md and kb/**/INDEX.md no longer
fails a reconcile or reaches the rebase-review gate: the log keeps both sides' entries,
the catalog and provenance are regenerated. Uncommitted work no incoming commit touches
rides through the rebase via --autostash; the working tree is backed up under
refs/wikitool/reconcile-backup first. is_generated is narrowed to kb/.

Files changed:
- CHANGES.md
- VERSION
- instructions/gates.md
- instructions/session-setup.md
- tools/CONTRACT.md
- tools/chemenu/commands/git_publish.py
- tools/chemenu/commands/index_build.py
- tools/chemenu/commands/provenance_cmd.py
- tools/chemenu/tests/test_git_publish.py

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2

VERSION

@@ -1 +1 @@
-8.0.0-beta.45
+8.0.0-beta.46