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

docs/reference/commands/README.md

@@ -97,6 +97,8 @@ Full records: [git.md](git.md)
 
 - [`sync`](git.md#sync) - Fetch `<remote>/<branch>` and bring the local branch up to date with it.
 - [`publish`](git.md#publish) - Reconcile with `<remote>/<branch>`, then stage all changes, commit, and push.
+- [`backup init`](git.md#backup-init) - Create the backup target's bare repository and make it `origin` when there is none.
+- [`backup run`](git.md#backup-run) - Mirror this machine's files that are not in git into `<target>/<machine>/`.
 
 ## Guideline export