Each wiki has three zones, plus a registry that lives outside every wiki and lists them all. The zones separate what you drop in from what the agent distills and from the operational state it keeps.
Folders you drop sources into. Configured per wiki
Read, add processed frontmatter, move per post_ingest rule
Structured knowledge
Projects, documentation, resources, people, concepts (whichever you enable)
Read and write
_service/
Manifest, log, hot list, source summaries, archives, feedback rules
Read and write
Entry points are the boundary between things you saved and things the agent has read. Structured knowledge holds the distilled pages the agent writes and you edit. The _service/ folder holds operational state that the agent maintains and mostly stays out of your way.
The registry at ~/.claude/obsidian-wiki/wiki-registry.json lists every wiki and its absolute root path. The plugin reads it on every invocation to resolve which wiki a command targets. It is set at the first /setup-wiki run and records the shared vault_root where the docs at <vault_root>/_service/docs/ live. See Entry points and Structured knowledge for what each zone does.
For the whole system at once, the plugin folder, the registry, the shared docs, one wiki blown up to show its three zones and config files, and the command groups, see the panopticon view.
Two files at each wiki root drive everything: CLAUDE.md (generic boilerplate, identical across every wiki) and wiki-config.md (yours). Every command reads both on every invocation. See Commands for what each verb does.
