backup: an instance backs up into a synced folder - backup init makes a bare repository under <target>/git its origin, backup run and publish mirror the machine data into <target>/<machine>/, doctor warns about .git in a synced folder (#186); 10.0.0-beta.10

Files changed:
- CHANGES.md
- INSTALL.md
- VERSION
- docs/explanation/configuration-tiers.md
- docs/how-to/README.md
- docs/how-to/back-up-to-a-synced-folder.md
- docs/reference/commands/README.md
- docs/reference/commands/git.md
- docs/reference/commands/instance-health.md
- docs/reference/configuration.md
- instructions/publish-cycle.md
- instructions/setup-instance.md
- tools/CONTRACT.md
- tools/README.md
- tools/chemenu/backup.py
- tools/chemenu/cli.py
- tools/chemenu/cli_contract.py
- tools/chemenu/commands/backup_cmd.py
- tools/chemenu/commands/doctor.py
- tools/chemenu/commands/git_publish.py
- tools/chemenu/config_shapes.py
- tools/chemenu/reference_doc.py
- tools/chemenu/tests/conftest.py
- tools/chemenu/tests/test_backup.py
- tools/chemenu/tests/test_config_shapes.py

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

instructions/publish-cycle.md

@@ -52,7 +52,12 @@ consistent.
   to commit locally with `--no-push`, and run that only on their answer. Never push by hand
   (AGENTS.md invariant 5): the next `publish` that reaches the remote sends the local commit
   together with whatever is new. A local-only instance, which has no remote at all, passes
-  `--no-push` on every call ([setup-instance.md](setup-instance.md), step 4).
+  `--no-push` on every call ([setup-instance.md](setup-instance.md), step 3).
+- **A `WARN` that the machine-data backup failed?** The commit and the push stand, and `publish`
+  exited 0. Show the user the line - it names the reason, a synced folder that is not there or not
+  writable, say. Do **not** run `publish` again: it would have nothing to push and back nothing up.
+  Once the user has fixed the cause, `tools/wikitool backup run` repeats the backup
+  ([docs/how-to/back-up-to-a-synced-folder.md](../docs/how-to/back-up-to-a-synced-folder.md)).
 - **Query or lint pass?** Neither auto-publishes. Run `publish` only if asked to.
 - **Nothing under `kb/` changed?** Skip steps 1 and 2; a change to `tools/` or `instructions/`
   does not affect the catalog.