init-wiki

name	init-wiki
description	Initialize a plain-markdown knowledge base (Wiki/) in the current repo. Use when the user says "init wiki", "set up knowledge base", "add wiki to this repo", or when starting a new project that needs a wiki. Also triggers when update-wiki or check-wiki is invoked but Wiki/ does not exist yet.

Wiki Initialization

Create a Wiki/ knowledge base in the current repo. The wiki is plain Markdown — no databases, no embeddings, no special tooling. Works on GitHub, in Obsidian, in any text editor.

Step 1 — Ask the user for domain folders

The core structure is fixed:

Wiki/
  Index.md
  Status.md
  Concepts/
  Resources/
  <Domain>/         ← user chooses these

Ask the user what domain-specific folders to create. Give examples based on the repo content:

• Math project: Systems/, Proofs/, Theorems/
• Formalization project: Systems/, Proofs/, Concepts/
• Software project: Architecture/, APIs/, Modules/
• Research project: Experiments/, Methods/, Datasets/

Also ask what the code directory should be called. Default is Code/, but some projects use Wolfram/, src/, Lean/, etc. This affects where the new-project skill creates code files.

If the user doesn't care, pick sensible defaults based on the repo.

Step 2 — Create the folder structure

Create all directories and seed files. Use empty .gitkeep files in folders that start empty (except Concepts/ and Resources/ which get populated via other skills).

Step 3 — Seed Index.md

# Wiki Index

Knowledge base for [project]. Updated after each substantial step.
All articles are **draft** until reviewed — see revision workflow.

## Status
- [Status](Status.md) — current state

## Work

Execution state (specs, tasks, per-session progress) lives in the top-level
`Work/` folder, not the Wiki. See `Work/README.md`.

## Concepts

(none yet)

## Resources

(none yet)

## Tour

Interactive guided walk through the project — say **"start tour"** to begin.
Tour data lives in `Tour/` (local, gitignored).

## [Domain Section]

(none yet)

One section per domain folder. Link format: [Title](Folder/File.md) — summary.

Step 4 — Seed Status.md

# Status

## Current state

Wiki initialized. No articles yet.

## Recent changes

(none yet)

## Open questions

(none)

Status.md summarizes the knowledge base. Execution state — active work, next tasks, blockers — lives in Work/README.md, not here.

Populate with real information if the repo already has content worth summarizing.

Step 5 — Update CLAUDE.md

Append the wiki section to the repo's CLAUDE.md (create the file if it doesn't exist). Use this template:

## Knowledge Base (Wiki)

Wiki/ is a plain-markdown knowledge base maintained by the LLM. Human-readable,
no special tooling needed.

### Maintenance rules

After every substantial step, the LLM:
1. Creates or updates relevant articles in Wiki/
2. Updates Wiki/Index.md
3. Updates Wiki/Status.md
4. Adds cross-links in See also sections

The wiki is documentation — the LLM keeps it accurate automatically.
No human sign-off needed for wiki prose. Every article carries a
`[ LLM Generated ]` marker directly under its `# Title`.

### Human revision (code & functionality)

The LLM always presents new code, functionality, and work specs to the user for
review. It does not silently overwrite user-edited content. The revision loop:
generate → present → wait for feedback → revise or proceed.

### Work items (execution state)

Multi-session work lives in the top-level `Work/` folder (spec / tasks /
progress per item), separate from the Wiki. Run `/next-session` in a fresh
session to do the next task. See `Work/README.md`.

### Resources

Wiki/Resources/ holds summaries with download/clone URLs and a ## Recover
section. Resources/ (gitignored) holds actual binary files.

To rebuild all resources from wiki: Scripts/recover_resources.sh
The script parses ## Recover sections from Wiki/Resources/*.md.

### Notebooks

LLM notebook artifacts live in NotebooksLLM/: the .md source (tracked) and the
generated .nb (gitignored via NotebooksLLM/*.nb) sit side by side. The plain
Notebooks/ folder is reserved for user-authored notebooks and is never touched
by the LLM. Scripts convert .md → .nb and optionally publish to Wolfram Cloud.
These are generated artifacts, not wiki articles — they do not go in Wiki/.

### Guided Tour

Say "start tour" for an interactive walk through the project. Tour/ is
created on demand (local, gitignored). Each section produces a narrative .md
and runnable code file. The LLM stops after each section for feedback.

If CLAUDE.md does not already contain a Semantic line breaks: line (a scaffolded project gets one from code_style_template.md), also append the source-formatting toggle so this repo carries the config:

## Source formatting

Semantic line breaks: **on**
<!-- When on, prose in source files — markdown (.md) and LaTeX/Typst (.tex/.typ) —
     uses one sentence per line (semantic line breaks): each sentence starts on its
     own source line. Source only; rendered output is unchanged. Set to **off** to
     wrap prose into filled paragraphs. Do not reflow paragraphs onto one line; a
     blank line still separates paragraphs. Detect with:
     grep -qiE 'semantic line breaks:[[:space:]]*\*{0,2}on' CLAUDE.md && echo on || echo off -->

Step 6 — Update .gitignore

Add these entries if not already present:

Tour/
Resources/
NotebooksLLM/*.nb

Exceptions: if the project has git submodules in Resources/, preserve them with lines like !Resources/SubmoduleName/.

Wiki/ itself is tracked. Tour/, Resources/ (binary files), and generated .nb files are gitignored.

Step 7 — Scan and seed articles

If the repo already has code, documentation, or other content:

1. Identify the main entities (modules, systems, proofs, experiments, etc.)
2. Create a short wiki article for each in the appropriate domain folder
3. Add entries to Index.md
4. Update Status.md with a real summary
5. Cross-link articles with relative markdown links in See also sections

Use the article format from the update-wiki skill.

Article format

# Title

One-paragraph summary.

## Details

Body. Use subsections as needed.

## See also

- [Other Article](../Folder/OtherArticle.md) — why it's related

No status headers on wiki articles — they're documentation, maintained automatically.

When CLAUDE.md has Semantic line breaks: on (the default), write seeded article prose one sentence per source line — see the Source formatting rule.

Backlink convention

Use standard markdown relative links so the wiki is clickable on GitHub:

[Article Title](../Folder/Article.md)

Paths are relative to the current file. Examples from Wiki/Systems/TM.md:

• Link to a proof: [TM → GS](../Proofs/TMtoGS.md)
• Link to a concept: [Simulation Encoding](../Concepts/SimulationEncoding.md)
• Link to a resource: [Moore 1991](../Resources/Moore1991.md)

From Wiki/Index.md (one level up from subfolders):

• [Turing Machine](Systems/TuringMachine.md)