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This guide walks through the full first-time setup: initializing your wiki, running the first compile, browsing the output, and wiring it into your agent instructions so Claude uses it automatically every session.
1

Initialize

Open Claude Code in your project directory and run:
/wiki-init
The plugin scans your project for markdown-heavy directories, samples 10–15 representative files, and proposes a custom article structure that fits your domain. For example:
  • A product team’s wiki might get: Summary — Timeline — Key Decisions — Experiments & Results — Gotchas — Open Questions — Sources
  • A research wiki might get: Summary — Key Findings — Methodology — Evidence — Gaps & Contradictions — Open Questions — Sources
You approve (or tweak) the proposed sections before anything is written. Once confirmed, the plugin writes .wiki-compiler.json to your project root and creates the output directory structure.
2

Compile

Run the compiler to build your first wiki:
/wiki-compile
The compiler reads all your source files, classifies them into topics, and writes one article per topic into your output directory. It also generates a schema.md that defines your wiki’s structure and naming conventions.
The first compile takes 5–10 minutes depending on how many files you have. After that, /wiki-compile is incremental — it only recompiles topics whose source files changed.
When it finishes, you’ll see a summary showing how many topics were created, how many source files were processed, and any concept articles discovered (cross-cutting patterns that span three or more topics).
3

Browse the wiki

Open the output directory in Obsidian (or any markdown viewer) and start with INDEX.md. It lists all compiled topic articles with a one-line summary of each.Each topic article includes coverage indicators so you know how thoroughly the wiki covers that section:
## Summary [coverage: high -- 15 sources]
...trust this, it's well-sourced...

## Experiments & Results [coverage: medium -- 3 sources]
...decent overview, check raw files for details...

## Gotchas [coverage: low -- 1 source]
...read the raw sources listed in this section directly...
Spot-check a few articles to confirm they accurately reflect your knowledge before wiring the wiki into your agent instructions.
4

Add to AGENTS.md

Once you’re satisfied with the output, add the following to your project’s AGENTS.md (or CLAUDE.md). Replace {your output path} with the path you configured during /wiki-init.
## Knowledge Base

A compiled knowledge wiki is available at `{your output path}/`.

**Session startup:** Read `wiki/INDEX.md` for a topic overview, then read
specific topic articles relevant to your current task.

**Using coverage indicators:** Each section has a coverage tag:
- `[coverage: high]` -- trust this section, skip the raw files.
- `[coverage: medium]` -- good overview, check raw sources for granular questions.
- `[coverage: low]` -- read the raw sources listed in that section directly.

**When you need depth:** Check the article's Sources section for links to
raw files. Only read raw sources for medium/low coverage sections or when
you need very specific detail.

**Never modify wiki files directly** -- they are regenerated by `/wiki-compile`.
After saving, Claude automatically reads the wiki at the start of every session — no extra commands needed. High-coverage sections save tokens by replacing raw file reads. Low-coverage sections point Claude to the exact raw files it needs.
Only add this after running /wiki-compile at least once and confirming the topic articles accurately reflect your knowledge base.

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What’s next

Commands

Full reference for all /wiki-* commands, including /wiki-ingest, /wiki-search, and /wiki-lint.

Adoption modes

Graduate from staging to recommended to primary as your trust in the wiki grows.

AGENTS.md integration

Detailed guide to wiring the wiki into your agent instructions.

Incremental updates

Keep the wiki current as your source files change.