Every settings field declares its tier; a value in the wrong file is an error naming
file, key and tier. A field naming a program or affecting a gate cannot be declared
instance. Secrets are references only: {"ref": "<name>"} via WIKITOOL_SECRET_<NAME> or
a user-only secrets file, {"ref": "op://..."} via op read (locked 1Password: exit 42).
The preflight records op as an optional tool. doctor gains one line per tier, docs
verify checks a committed wikitool.json for plaintext secrets, CI resolves a real
op:// value through 1password/load-secrets-action. No feature reads its settings
this way yet; without the two files every other command is unchanged.
Files changed:
- .gitea/workflows/ci.yml
- .gitignore
- AGENTS.md
- CHANGES.md
- INSTALL.md
- VERSION
- docs/explanation/README.md
- docs/explanation/configuration-tiers.md
- docs/how-to/README.md
- docs/how-to/use-1password-for-settings.md
- docs/reference/commands/README.md
- docs/reference/commands/configuration.md
- docs/reference/commands/instance-health.md
- docs/reference/commands/types-instructions-and-docs.md
- docs/reference/configuration.md
- docs/reference/exit-codes.md
- instructions/dev/doc-pull-through.md
- instructions/dev/testing-conventions.md
- instructions/preflight.md
- tools/CONTRACT.md
- tools/README.md
- tools/chemenu/cli.py
- tools/chemenu/cli_contract.py
- tools/chemenu/commands/_util.py
- tools/chemenu/commands/config_cmd.py
- tools/chemenu/commands/docs_verify.py
- tools/chemenu/commands/doctor.py
- tools/chemenu/config.py
- tools/chemenu/config_shapes.py
- tools/chemenu/prerequisites.py
- tools/chemenu/settings.py
- tools/chemenu/tests/conftest.py
- tools/chemenu/tests/test_dist_cmd.py
- tools/chemenu/tests/test_preflight.py
- tools/chemenu/tests/test_preflight_pwsh.py
- tools/chemenu/tests/test_settings.py
- tools/chemenu/toolpaths.py
- tools/preflight.ps1
- tools/preflight.sh
- tools/prerequisites.txt
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2
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How-to guides
Task-oriented pages for the operator of an instance: one goal per page - upgrade an instance,
set up the MCP read server, run a weekly review - with the steps a human takes and the sentence
handed to the agent. A how-to guide never retells an agent's procedure: the steps an agent runs
live in instructions/, and a guide here says what to prepare, what to ask for and where the
agent stops.
Working with the wiki:
- Ingest a source - a file, a folder, a web page, or a document submitted through the MCP server
- Capture documentation from a git repository - and keep it current
- Export guidelines to captured repositories
- Query the wiki - asking, and searching yourself
- Maintain the wiki - lint, provenance, and the gates on the way to a publish
- Run the weekly review - commitments in a task tracker against the project pages
- Browse the wiki in Obsidian - and how pages are named
Running the instance:
- Update an instance - to a newer release of the stack
- Troubleshoot an instance
- Set up the MCP read server - for a consumer that is not a terminal on this machine
- Trace and score agent sessions
- Use 1Password for settings - secrets and private values out of the tree, on the desktop and in CI
Installing a new instance is INSTALL.md at the repository root.