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

instructions/session-setup.md

@@ -85,7 +85,11 @@ than one machine or session writes to. Running `sync` first shrinks that window
 the session instead of discovering the drift only at the very end.
 
 `sync` fetches the remote and fast-forwards or rebases automatically when that is safe; it
-never commits and never pushes. **Exit 42 (rebase-review)?** Same as any exit 42 - read the
+never commits and never pushes. Files `wikitool` generates are never a reason to stop: when the
+catalog or `kb/log.md` changed on both sides, `sync` keeps both sides' log entries and
+regenerates the catalog and `kb/provenance.md`, which it leaves as an uncommitted change for the
+next `publish`. Uncommitted work that the incoming commits do not touch stays where it is.
+**Exit 42 (rebase-review)?** Same as any exit 42 - read the
 diff it prints, judge whether it conflicts with what you are about to do, summarize that to the
 user, then `tools/wikitool sync --confirm-rebase <token>` before continuing. See
 [gates.md](gates.md).