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
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Task-oriented pages for the operator of an instance: one goal per page - upgrade an instance,
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set up the MCP read server, run a weekly review - with the steps a human takes and the sentence
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handed to the agent. A how-to guide never retells an agent's procedure: the steps an agent runs
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live in `instructions/`, and a guide here says what to prepare, what to ask for and where the
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agent stops.
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Working with the wiki:
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- [Ingest a source](ingest-a-source.md) - a file, a folder, a web page, or a document submitted
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through the MCP server
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- [Capture documentation from a git repository](capture-repository-docs.md) - and keep it current
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- [Export guidelines to captured repositories](export-guidelines.md)
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- [Query the wiki](query-the-wiki.md) - asking, and searching yourself
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- [Maintain the wiki](maintain-the-wiki.md) - lint, provenance, and the gates on the way to a publish
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- [Run the weekly review](run-the-weekly-review.md) - commitments in a task tracker against the
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project pages
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- [Browse the wiki in Obsidian](browse-with-obsidian.md) - and how pages are named
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Running the instance:
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- [Update an instance](update-an-instance.md) - to a newer release of the stack
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- [Troubleshoot an instance](troubleshoot.md)
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- [Set up the MCP read server](set-up-the-mcp-server.md) - for a consumer that is not a terminal
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on this machine
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- [Trace and score agent sessions](trace-and-score-sessions.md)
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- [Use 1Password for settings](use-1password-for-settings.md) - secrets and private values out
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of the tree, on the desktop and in CI
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Installing a new instance is [INSTALL.md](../../INSTALL.md) at the repository root.
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