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

CHANGES.md

@@ -59,7 +59,7 @@ concern - readable here, never shipped as something to parse.
 
 ---
 
-## 8.0.0-beta.45 - 2026-10-06 - kb/CONVENTIONS.md.template: the guideline filter is a default, not a setup question
+## 8.0.0-beta.46 - 2026-10-06 - publish/sync merge generated files mechanically and carry non-overlapping uncommitted work through a rebase
 
 **Author:** Torben Nehmer
 
@@ -111,6 +111,7 @@ concern - readable here, never shipped as something to parse.
 - raw capture / raw status / --replaces-bundle: documentation from git repositories as a bundle, with drift reporting
 - wiki-ingest: updating the captured repositories is a step-1 branch over raw status
 - export guidelines: the guideline pages as a generated GUIDELINES.md, pushed into the captured repositories behind the Guideline Push Gate
+- publish/sync merge generated files mechanically and carry non-overlapping uncommitted work through a rebase
 
 **Low impact**
 - version bump no longer points at version release in its output
@@ -158,6 +159,47 @@ concern - readable here, never shipped as something to parse.
 - kb/CONVENTIONS.md.template: the guideline filter is a default, not a setup question
 <!-- /wikitool:bumps -->
 
+### publish/sync merge generated files mechanically and carry non-overlapping uncommitted work through a rebase
+
+Every ingest touches `kb/index.md` and `kb/log.md`, so two ingests on two checkouts - or two
+sessions - always "overlapped", in files that carry no decision. `reconcile` (behind `sync` and
+both of `publish`'s reconciles) failed on all three shapes of that: an uncommitted ingest stopped
+the fast-forward with exit 1; two committed ingests went to the rebase-review gate and, once
+cleared, failed on the two appends at the end of the log; and any uncommitted file at all made
+`git rebase` refuse, so a stranded commit plus a new ingest could not be published.
+
+- **Generated files never count as an overlap.** The rebase-review gate, its token and its diff
+  leave out `kb/index.md`, `kb/log.md`, `kb/provenance.md` and every `kb/**/INDEX.md`; an
+  overlapping *non*-generated file still goes to review.
+- **Where they are what stops git, they are merged mechanically.** Uncommitted generated files
+  are set aside (the log's appended bytes kept, the rest discarded); rebase conflicts in them are
+  resolved step by step - the catalog and provenance take the side being rebased onto, the log
+  takes that side plus what the replayed commit appended. Afterwards the log gets the set-aside
+  entries back at its end and the catalog and `kb/provenance.md` are regenerated in-process, left
+  as an uncommitted change. `index rebuild` and `sources rebuild-index` lend their writing half
+  for that as `index_build.write_index` and `provenance_cmd.write_provenance_index`.
+- **Uncommitted work no incoming commit touches rides through a rebase** (`git rebase
+  --autostash`) and comes back byte-identical.
+- **Before the first write, the working tree is stored** as a commit under
+  `refs/wikitool/reconcile-backup`; a success drops it, a failure restores the working tree and
+  names the ref.
+- **`publish`'s retry after a rejected push** commits the regenerated files on their own before
+  the second push, since staging is long past by then.
+- **Unchanged where git manages on its own:** a reconcile that succeeded before runs the same git
+  command and regenerates nothing - `index rebuild` stamps today's date into `kb/index.md`, and a
+  rebuild there would leave every `sync` with a modified file. A log edited rather than appended
+  to, or an uncommitted change on a path the incoming commits change, stops exactly as before.
+- **`is_generated` is narrowed to `kb/`**, as AGENTS.md invariant 1 already defines it: an
+  `INDEX.md` in a captured repository under `raw/` is source material, counted by the Mass-Update
+  Gate and never discarded.
+
+Drop-in: no command, flag, file format or state file changes, and the previous version ignores a
+leftover backup ref. Cases that ended in exit 1 or 42 now go through. A `--confirm-rebase` token
+issued before the update may read as stale afterwards, because the overlap it covers no longer
+lists generated files - the gate then asks again, as for any stale token. `sync`'s and
+`publish`'s records, `instructions/session-setup.md` and `instructions/gates.md` follow (Gitea
+#180).
+
 ### kb/CONVENTIONS.md.template: the guideline filter is a default, not a setup question
 
 The § Guidelines for other repositories section shipped with a `{...}` placeholder, and