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feat: docs reference generates a human command reference under docs/reference/ from the command records, one page per group plus exit codes and gates; toc never lands inside another generated region (#188)
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- CHANGES.md
- README.md
- VERSION
- docs/reference/README.md
- docs/reference/commands/README.md
- docs/reference/commands/catalog-and-log.md
- docs/reference/commands/content-migrations.md
- docs/reference/commands/distribution-and-versioning.md
- docs/reference/commands/finding-and-checking.md
- docs/reference/commands/git.md
- docs/reference/commands/guideline-export.md
- docs/reference/commands/instance-health.md
- docs/reference/commands/links-and-citations.md
- docs/reference/commands/pages.md
- docs/reference/commands/provenance.md
- docs/reference/commands/raw-material-and-uploads.md
- docs/reference/commands/telemetry.md
- docs/reference/commands/types-instructions-and-docs.md
- docs/reference/commands/workshop-runs-and-session-budget.md
- docs/reference/exit-codes.md
- instructions/dev/doc-pull-through.md
- tools/CONTRACT.md
- tools/README.md
- tools/chemenu/cli.py
- tools/chemenu/cli_contract.py
- tools/chemenu/commands/docs_verify.py
- tools/chemenu/reference_doc.py
- tools/chemenu/tests/test_reference_doc.py
- tools/chemenu/toc.py

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2
2026-10-06 21:29:01 +02:00

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Markdown

# Git
Pulling in the remote and publishing a change - the only way a change leaves this checkout.
<!-- wikitool:toc -->
## Contents
- [`sync`](#sync)
- [`publish`](#publish)
<!-- /wikitool:toc -->
<!-- wikitool:reference-commands -->
## `sync`
Fetch `<remote>/<branch>` and bring the local branch up to date with it.
**Synopsis**
- `wikitool sync [--remote origin] [--branch main] [--confirm-rebase TOKEN]`
**Options**
```text
--remote <str> Git remote to reconcile against [default: origin]
--branch <str> Branch to reconcile [default: main]
--confirm-rebase TOKEN Clear the rebase-review gate for the exact upstream
state and file overlap this token was issued for. The
token comes from the gate's own refusal output.
-h, --help Show this message and exit.
```
**Examples**
```bash
tools/wikitool sync
tools/wikitool sync --confirm-rebase <token> # re-run after exit 42, once the user approved
```
**Behaviour**
- Fetches `<remote>/<branch>`, then: fast-forwards when only the remote moved; rebases the local commits on top when both sides moved but touched disjoint files; exits 42 (rebase-review gate) when both sides touched the same file.
- Files `wikitool` generates (`kb/index.md`, `kb/log.md`, `kb/provenance.md`, every `kb/**/INDEX.md`) never count as an overlap and never reach the gate. Where they are what stops git - uncommitted ones in the way of a fast-forward or rebase, or a rebase conflict in them - they are merged mechanically: `kb/log.md` becomes the incoming log plus the entries only this side appended, and the catalog and `kb/provenance.md` are regenerated from the merged pages and left as an uncommitted change. A reconcile git can do on its own is unchanged and regenerates nothing.
- Uncommitted changes that no incoming commit touches do not stop a rebase: they are carried through it (`git rebase --autostash`) and come back unchanged.
- Before anything is set aside, the working tree is stored as a commit under `refs/wikitool/reconcile-backup`. A successful reconcile drops it; a failed one restores the working tree and names the ref.
- A refused call performs no rebase attempt and leaves the branch where it was.
- The `--confirm-rebase` token covers the exact upstream state and the set of files touched on both sides, generated files excluded; either one moving makes it stale.
- Makes no commit, no push, and no forced operation of any kind.
- Three messages for a fetch that fails: no remote of that name, a remote that answers but has no such branch yet (a new, empty repository), and a remote that cannot be reached. All three exit 0 here; `publish` stops on the first and the last.
- Run it once at the start of a writing session.
**Properties**
- Changes files: yes
- Idempotent: yes
- Atomic: No - fetch, then at most one merge/rebase attempt, aborted cleanly on failure with the working tree restored; a success that merged generated files then rewrites the catalog
- Counts toward the session call budget: yes
- Can reach the network: yes
- Gates: rebase-review - see [exit codes and gates](../exit-codes.md)
**Exit codes**
- `0` - success
- `0` - No remote configured - reported and skipped, not a failure
- `0` - The remote cannot be reached - reported and skipped, not a failure
- `1` - The automatic rebase hit a real conflict outside the generated files (git failed), or `kb/log.md` was edited rather than appended to; it is aborted cleanly and the working tree restored
- `1` - An uncommitted change - or an untracked file - sits on a path the incoming commits also change; nothing was changed
- `42` - Rebase-review gate: `<remote>/<branch>` moved and both sides changed the same file, generated files aside; the output lists the upstream commits, the overlapping files and their diff
**See also**
- `wikitool publish` - runs the same reconcile before it commits and pushes
- `instructions/session-setup.md` - where a session runs `sync`
- `instructions/gates.md` - the gate procedure
## `publish`
Reconcile with `<remote>/<branch>`, then stage all changes, commit, and push.
**Synopsis**
- `wikitool publish --message "<op>: <desc>" [--no-push] [--confirm TOKEN] [--confirm-rebase TOKEN] [--threshold N] [--remote origin] [--branch main] [--path P ...]`
**Options**
```text
--message <str> Commit message summary, e.g. 'ingest: docker-
cheatsheet' [required]
--push / --no-push [default: push]
--confirm TOKEN Clear the Mass-Update Gate for the exact changeset
this token was issued for. The token comes from the
gate's own refusal output - run without it first to
see the file list, show that output to the user, and
only pass this once they have approved it.
--confirm-rebase TOKEN Clear the rebase-review gate raised by the pre-push
reconcile step. The token comes from that gate's own
refusal output - see `tools/wikitool sync`.
--threshold <int> Mass-Update Gate threshold: number of counted files
at/above which clearance is required. [default: 10]
--remote <str> Git remote to push to [default: origin]
--branch <str> Branch to push [default: main]
--path <str> Limit this publish to a path (repeatable). Lets a
large change be committed in reviewable batches
instead of one opaque commit - the Mass-Update Gate
then counts only the files in scope.
-h, --help Show this message and exit.
```
**Examples**
```bash
tools/wikitool publish --message "ingest: docker-cheatsheet"
tools/wikitool publish --confirm <token> --message "ingest: docker-cheatsheet" # re-run after a Mass-Update exit 42, once the user approved
tools/wikitool publish --confirm-rebase <token> --message "ingest: docker-cheatsheet" # re-run after a rebase-review exit 42, once the user approved
```
**Behaviour**
- Order: branch check and Publish-Remote Gate, then the reconcile with `<remote>/<branch>`, then the Mass-Update Gate, then `git add -A`, commit and push. `--no-push` skips all but the Mass-Update Gate and the commit.
- Without `--no-push`, a remote that is not configured or cannot be reached ends the call with exit 1 at the reconcile - before the gate, `git add` and the commit, and also on a clean tree. Nothing is committed, the index and the working tree are unchanged, and the message names `--no-push` as the way to a local commit. The next `publish` that reaches the remote pushes that commit along with whatever is new. A remote that answers but has no `<branch>` yet (a new, empty repository) is not this case: the first publish of an instance commits and pushes as before.
- Reconcile: fetches `<remote>/<branch>`, fast-forwards when only the remote moved, rebases the local commits on top when both sides moved but touched disjoint files, and exits 42 (rebase-review gate) when both sides touched the same file. A refused reconcile performs no rebase attempt. The `--confirm-rebase` token covers the exact upstream state and the set of files touched on both sides.
- Generated files are never an overlap: where they are all that stops the reconcile, it merges them as `sync` does (both sides' log entries kept, the catalog and `kb/provenance.md` regenerated) and carries uncommitted changes no incoming commit touches through the rebase. The proactive reconcile runs before staging, so this publish commits the regenerated files - with `--path` too, see there; on the retry after a rejected push they get a commit of their own before the second push.
- The push target must be the checked-out branch; this is checked before anything is staged. The unborn branch of a fresh `git init -b main` counts as checked out, so the first publish of a new instance works; a real detached HEAD is refused.
- With nothing new to stage, a local commit the remote lacks is still pushed: one left behind by an earlier publish whose push failed, or every commit when the remote answers but does not have the branch yet (a new, empty remote repository).
- A rejected push that finds the remote unreachable on its one retry reports the original push error.
- A rejected push gets exactly one more reconcile-and-push; never more than one.
- Mass-Update Gate: counts the files that would be committed, refuses with exit 42 at `--threshold` (default 10) or more, and prints a review report - a scale line (file count, total lines added/removed, status breakdown), attention notes where they apply (deletions by name, control-plane and harness-config touches, published pages, the largest single change, binaries), and every counted path grouped by area with its status and churn. The list is what the commit will hold: it is computed from a scratch copy of the index after `git add -A`, so a path that is staged as deleted and back in the working tree is not counted twice, and a rename counts as its old path deleted plus its new path added. The real index and the working tree are not touched, so a refused publish leaves both byte-identical.
- Never counted and never shown for approval, but committed like everything else: anything under `work/`, and the files `wikitool` generates itself (`kb/index.md`, `kb/log.md`, `kb/provenance.md`, every `INDEX.md` under `kb/`). The refusal line accounts for both, by reason.
- The `--confirm` token covers each counted path, the blob id of its contents and the publish target: a different file list or edited contents need a new clearance.
- Publish-Remote Gate: when the checkout carries `.wikitool-remotes.json` and the push URL of `--remote` is not listed in it, exits 42 before the reconcile fetches anything. The URL is read with `git remote get-url --push`, so a repointed remote does not pass on its name. An absent file means unrestricted; a malformed one is an error, not permission.
- `--path` (repeatable) scopes the whole operation - gate count, staging and commit - to that subtree, with one exception: uncommitted generated files outside `--path` (`kb/index.md`, `kb/log.md`, `kb/provenance.md`, every `INDEX.md` under `kb/`) are staged and committed too, and a line names them - whether a reconcile or the change itself wrote them. They stay out of the gate count, and the `--confirm` token and the re-run line cover the `--path` given. Every other file outside `--path` is left as it is.
- Commit message: `--message`, then a `Files changed:` paragraph listing every committed path. When `--message` ends in a paragraph git reads as a trailer block (`Co-Authored-By:` and the like), that block stays the last paragraph and the list goes in front of it, since git reads trailers from the last paragraph only. `git interpret-trailers` decides whether there is such a block, and the list moves only when git reads the same trailers from the result; otherwise it is appended at the end. `--message` is not part of any gate token.
- After a successful commit or push whose changed files include `tools/`, `types/`, `instructions/`, `AGENTS.md` or a path ending in `CONTRACT.md`, prints one reminder line: the phase past this point (an issue-body rewrite, `docs/` staleness, a changelog entry's accuracy) is not covered by `docs verify`, `instructions verify` or `pytest`. It is not a gate: no exit code change, nothing to clear, and silent for an ordinary content publish.
**Properties**
- Changes files: yes
- Idempotent: no
- Atomic: No - sequential git operations. Every gate runs before staging, except on the one retry of a rejected push, where the rebase-review gate can exit 42 after the commit: nothing is pushed, and the re-run with `--confirm-rebase` pushes that commit
- Counts toward the session call budget: yes
- Can reach the network: yes
- Gates: mass-update, publish-remote, rebase-review - see [exit codes and gates](../exit-codes.md)
**Exit codes**
- `0` - success
- `1` - git failed - `git add`, `git commit`, `git push`, or the reconcile's automatic rebase (a conflict outside the generated files, an edited `kb/log.md`, or an uncommitted change on a path the incoming commits change)
- `1` - The push target (`--branch`) is not the checked-out branch, or HEAD is detached; the unborn branch of a fresh `git init` is not this case
- `1` - No `--no-push`, and the remote is not configured or cannot be reached; nothing was committed
- `1` - `--yes`/`-y` was passed - the flag does not exist and fails with an explicit error
- `1` - `.wikitool-remotes.json` is unreadable or has no usable `allowed_push_urls` list
- `42` - Mass-Update Gate: `--threshold` (default 10) or more counted files would be committed, or the `--confirm` token does not match this changeset
- `42` - Rebase-review gate: `<remote>/<branch>` moved and both sides changed the same file; the output lists the upstream commits, the overlapping files and their diff
- `42` - Publish-Remote Gate: `.wikitool-remotes.json` exists and the push URL of `--remote` is not listed in it, or `--remote` resolves to no push URL
**See also**
- `wikitool sync` - the same reconcile on its own, without committing or pushing
- `instructions/gates.md` - the gate procedure
- `instructions/setup-instance.md` - the first publish of a new instance
<!-- /wikitool:reference-commands -->