PDF is read with pypdf (page markers, scan warning, encrypted files refused), Outlook .msg with olefile as a container like an .eml, and a .msg attached to a mail is quoted. Both packages are in tools/requirements.txt and imported only when such a file is derived, so a missing one stops that format alone. doctor reports one import-filter line per package-backed format. Files changed: - CHANGES.md - VERSION - docs/how-to/ingest-a-source.md - docs/reference/commands/instance-health.md - docs/reference/commands/raw-material-and-uploads.md - tools/CONTRACT.md - tools/README.md - tools/chemenu/commands/doctor.py - tools/chemenu/commands/raw_cmd.py - tools/chemenu/filters/__init__.py - tools/chemenu/filters/mail.py - tools/chemenu/filters/msg.py - tools/chemenu/filters/pdf.py - tools/chemenu/tests/binary_formats.py - tools/chemenu/tests/test_raw_derive_binary.py - tools/requirements.txt Co-Authored-By: Claude Code <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2
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
Installing a new instance is INSTALL.md at the repository root.