Wiki Init

Wiki Init

Bootstrap a new LLM-maintained wiki at a user-specified path.

Pre-flight

Check whether a SCHEMA.md already exists nearby. If yes, ask the user if they want to reinitialize or just continue with the existing wiki.

Process

1. Gather configuration (one question at a time)

Ask:

1. Where should the wiki live? (absolute path, e.g. ~/wikis/ml-research)

2. What is the domain/purpose? (one sentence)

3. What types of sources will you add? (papers, URLs, code files, transcripts, etc.)

4. What categories should index.md use?

   • Research default: Sources | Entities | Concepts | Analyses
   • Codebase default: Modules | APIs | Decisions | Flows — see codebase.md in this skill's directory for detailed codebase guidance
   • Or specify custom

5. How will you primarily browse this wiki?

   1. Obsidian (or another [[wiki-link]]-aware viewer) — uses [[slug]] syntax
   2. GitHub / VS Code preview / static-site generator / plain markdown — uses [[slug](pages/slug.md)] syntax

   The choice is recorded in SCHEMA.md as link_style: obsidian or link_style: markdown and applied by every other wiki skill.

2. Create directory structure

<wiki-root>/
├── SCHEMA.md         ← conventions + absolute path (how other skills find the wiki)
├── config/
│   └── link-style.md ← cross-reference emit/parse rules (copied from this skill)
├── .gitignore        ← local-only / generated artifacts (audit reports, index) excluded from version control
├── bin/                  ← helper scripts (copied verbatim from this skill's assets/bin/)
│   ├── generate-index.py  ← regenerates wiki/index.md from page frontmatter (stdlib only)
│   ├── render-log.py      ← renders the operation log from git history (stdlib only)
│   ├── check-contradictions.py ← pre-commit gate: blocks staged pages flagged as contradicting
│   ├── lint-mechanical.py ← deterministic lint checks; full mode (JSON for wiki-lint) + --staged gate
│   └── hooks/pre-commit   ← tracked git hook chaining both gates (wired via core.hooksPath)
├── raw/              ← immutable source documents (you add these, LLM never modifies)
├── wiki/
│   ├── index.md      ← GENERATED catalog (gitignored) — never hand-edit; run bin/generate-index.py
│   ├── log.md        ← operation log — ONLY for non-git wikis (git wikis use git history)
│   ├── overview.md   ← evolving synthesis of everything known
│   └── pages/        ← all wiki pages, flat, slug-named (NO subdirectories)
└── assets/           ← downloaded images, PDFs, attachments

Critical: wiki/pages/ is flat. All pages live here as <slug>.md. No subdirectories. Slugs are lowercase, hyphen-separated.

Copy the chosen link-style rule file into the wiki:

• If user picked option 1 (Obsidian): copy this skill's config/link-style-obsidian.md to <wiki-root>/config/link-style.md.
• If user picked option 2 (markdown): copy this skill's config/link-style-markdown.md to <wiki-root>/config/link-style.md.

Only one file is copied — the chosen one — and it is renamed to link-style.md in the wiki. Every other wiki skill reads from <wiki-root>/config/link-style.md to know how to emit and parse cross-references.

Ensure <wiki-root>/.gitignore excludes generated and local-only artifacts (audit reports and the generated index) — if the wiki is or later becomes a git repo, this keeps disposable artifacts out of version control. Do not clobber an existing .gitignore — a reinitialized wiki, or a wiki root nested in an existing git repo, may already have one:

• If <wiki-root>/.gitignore does not exist, create it with the block below.
• If it exists but is missing either ignore line, append whichever line(s) it lacks.
• If it already ignores both, leave it untouched.

# Audit reports are regenerated local-only artifacts (wiki-audit). The committed record
# of an audit is the `review:` frontmatter token on the audited page, not the report.
wiki/pages/audit-*.md
# index.md is generated from page frontmatter by bin/generate-index.py — a runtime
# artifact, regenerated on demand. The source of truth is each page's frontmatter.
wiki/index.md

This is the same create-or-append discipline wiki-audit uses to self-heal (Task 4).

3. Write SCHEMA.md

# Wiki Schema

## Identity
- **Path:** <absolute path to wiki-root>
- **Domain:** <user's domain description>
- **Source types:** <list>
- **Created:** <YYYY-MM-DD>

## Page Frontmatter
Every wiki page must start with:
---
title: <page title>
category: <one of the Index Categories below>
summary: <one-line description — becomes this page's index entry>
tags: [tag1, tag2]
sources: [source-slug1]
created: YYYY-MM-DD
updated: YYYY-MM-DD
---

`category` and `summary` drive index generation (see **Index Generation** below);
`category` must match one of the wiki's Index Categories. `created` is set once when the
page is first written and never changes; `updated` bumps on every edit.

## Cross-References
- **link_style:** <obsidian | markdown — the user's choice from step 1, question 5>
- **link_style_rules:** config/link-style.md
- See `config/link-style.md` for the exact emit and parse rules. Every wiki skill
  reads that file to decide how to write new cross-references and how to scan
  existing ones.

## Concept Identity

The slug **is** the concept's identity — there is no separate id. A concept is the
page at `wiki/pages/<slug>.md`; everything that links to it uses `[[slug]]`. This only
works if the link graph is trustworthy, so two rules hold everywhere links are written:

1. **Links are verified, never invented.** Before writing any `[[slug]]`, the slug must
   resolve to an existing `wiki/pages/<slug>.md` **or** to a page being created in the
   same operation. List the existing page set first (`ls wiki/pages/`); never emit a
   link to a slug you have not confirmed. A `[[slug]]` that resolves to nothing is a
   hallucinated link — the failure this discipline exists to prevent.

2. **Homonyms get qualified slugs.** When a new concept collides with an existing slug
   for a *different* sense, qualify both with a discriminator rather than overloading
   one page:
   - `mercury-planet` / `mercury-element` / `mercury-mythology`
   - `transformer-ml` / `transformer-electrical`

   Pick the narrowest discriminator that disambiguates. `wiki-lint` warns when slugs
   sharing a base token look like an unintended collision.

Consolidating two pages that turn out to be the same concept (merge), or separating one
overloaded page into qualified pages (split), is the job of the `wiki-merge` skill.

## Citations

Cite every non-common-knowledge factual claim. "Common knowledge" = uncontroversial,
undergraduate-level facts in this wiki's domain. Granularity is paragraph or claim,
never per-sentence. If you cannot produce a citation in one of the forms below,
find one, weaken the claim, or drop it.

Format: Markdown footnotes. Two citation kinds, three valid targets.
The slug-target form below follows the `link_style` declared above; the examples
shown here use that style.

**Quote citation** (preferred):

The model uses 8 attention heads.[^1]

Synthesis citation (when no single quote captures the claim):

The architecture is fundamentally an encoder-decoder with attention.[^2]

<if link_style: obsidian>
[^2]: [[attention-is-all-you-need]] §3.2-3.4 [synthesis] L138-202 — encoder, decoder, and
      attention sections together describe the full multi-head architecture
<if link_style: markdown>
[^2]: [[attention-is-all-you-need](pages/attention-is-all-you-need.md)] §3.2-3.4 [synthesis] L138-202 — encoder, decoder, and
      attention sections together describe the full multi-head architecture

L142-143 / L138-202 are line ranges in the raw source file. For a quote they mark the lines the quote is taken from; for a synthesis they mark the block being summarized.

Three rules for every footnote:

1. The cited target is one of three forms:

   • A slug reference to a source-type wiki page, written in the wiki's link_style (preferred for sources you've ingested via wiki-ingest)
   • raw/<file> or assets/<file> — a path to a local file (for drive-by citations where a synthesis page isn't worth creating)
   • <URL> — a live URL, tweet, or ephemeral source (no local copy required)

   Never cite entity, concept, or analysis pages — those are syntheses, not sources.

2. A locator is present. Always a semantic locator: §<section>, p.<n>, [HH:MM:SS] for transcripts, URL anchor for web, or (YYYY-MM-DD) for dated posts.

   Plus a line-range when the source is text-addressable. If the resolved raw file is markdown, plaintext, code, or cached HTML, append a line-range token after the semantic locator:

   • L<start>-<end> — a range, e.g. L142-145
   • L<n> — a single line, e.g. L142
   • L142-145,L201-203 — disjoint ranges

   The line range refers to lines in the raw source file resolved from the target ([[slug]] → its **Source:** raw path; or a direct raw/<file>/assets/<file>). raw/ is immutable, so these line numbers are stable references.

   A line-range is required for text-addressable sources and applies to BOTH citation kinds — a [synthesis] footnote marks the block it summarizes with L… just as a quote marks the lines it quotes. Exempt (semantic locator only, no L…): PDFs, transcripts, and live URLs with no local cached copy.

3. Either a verbatim quote, or the [synthesis] tag plus a description of what the cited range supports. No third option.

Drive-by citation examples:

[^3]: raw/scaling-laws.pdf p.7 — "loss scales as a power law in compute"
[^4]: https://twitter.com/user/status/123 (2026-04-15) — "<tweet text>"

Cross-Model Review

wiki-audit strong runs a second-opinion pass with a different-provider model and stamps the audited page with an optional review: frontmatter block:

review:
  model: codex          # gemini | claude-sonnet
  provider: openai      # google | anthropic
  date: YYYY-MM-DD
  status: clean         # or: disputed
  findings: 2           # present only when status: disputed

• status: clean — the reviewer surfaced no disagreement with the normal audit.
• status: disputed — the reviewer flagged overreach or a contradiction the normal audit missed; findings: carries the count. The detail lives in the (local-only) audit report.
• provider: anthropic (the claude-sonnet fallback) means no different-provider CLI was available, so the check is same-provider and weaker.

This block is optional and is added only by wiki-audit strong. Pages never need it to be valid.

Contradiction Check

wiki-ingest runs a cheap contradiction check on the pages each ingest touches, before it commits. It is a gate, not an annotation: every page that lands in git is clean.

• Scope — touched neighbors only. The check compares the pages an ingest wrote or edited against (a) themselves and (b) the pages that ingest already read (the entity / concept pages it updated and the neighbor pages from its backlink audit). It does NOT re-read the whole wiki — a conflict with a distant, untouched page is left to the periodic wiki-lint sweep.
• Blocking vs. soft. A blocking contradiction is a real factual conflict on the same entity under the same scope — incompatible dates, counts, names, or mutually-exclusive claims. A soft tension (differing emphasis, values within plausible version / measurement variance, claims that hold under different scope) is not a conflict.
• The transient blocker flag. When a blocking contradiction is found, a single line is written to the affected page's frontmatter and the ingest stops before committing:

  contradiction-check: failed — <one-line reason naming the counterpart [[slug]] or "internal">
  

  The machine-readable token is the literal contradiction-check: failed. It exists ONLY while the conflict is unresolved; resolving the conflict removes the line. A committed page never carries it — there is no passed stamp, no severity history, nothing. Absence of the flag is the only "clean" state.
• Soft tensions are surfaced, not recorded — mentioned in the ingest summary so you can act if you wish, but never persisted and never blocking.

This flag is also what the Pre-commit Gate below scans staged files for.

Pre-commit Gate

On a git wiki, bin/hooks/pre-commit (installed by wiki-init via git config core.hooksPath bin/hooks) runs two deterministic gates before every commit — no LLM:

1. bin/check-contradictions.py — scans the staged content of wiki/pages/*.md, frontmatter only, and blocks the commit if any page still carries a contradiction-check: failed flag. Backstop to the skill-level hold in wiki-ingest step 7b; on a healthy wiki it never fires. Resolve the contradiction and remove the contradiction-check: line, then re-stage.
2. bin/lint-mechanical.py --staged — scans the staged pages for structural problems and blocks the commit on any: missing required frontmatter, a broken [[link]], or a slug collision (a bare slug clashing with a qualified one). Fix the page and re-stage.

• Fresh clone: core.hooksPath is repo-local config and is not cloned — re-run git config core.hooksPath bin/hooks once after cloning.
• Override an intentional commit with git commit --no-verify.

Operation Log & Commit Convention

Operations: init, ingest, query, update, lint, audit, merge, split

Git wiki — the git history is the operation log. After an operation, the skill suggests a commit message and commits on your confirmation (skills never auto-commit). Render the human log on demand with python bin/render-log.py.

The suggested subject line follows the repo's commit convention:

1. Detect an existing convention first — scan recent git log and any .gitmessage, commitlint config, or CONTRIBUTING.md. If the repo already has a subject style, follow it.

2. Default to Conventional Commits when none is found, choosing the type by operation:

   Operation	Type
   init	chore
   ingest	docs
   update	docs
   query (saved)	docs
   lint	fix if fixes applied, else chore
   audit	fix if fixes applied, else chore
   merge / split	refactor

Always append a Wiki-Op: trailer, whatever the subject style — it is what render-log.py keys on, decoupling the log from the subject convention. Which pages changed is read from the commit diff, so no Pages: trailer is needed.

docs: summarize Attention Is All You Need

Wiki-Op: ingest

Non-git wiki — fallback to wiki/log.md. Append one entry per operation: ## [YYYY-MM-DD] <operation> | <title>.

Index Generation

wiki/index.md is a generated, gitignored artifact — never hand-edit it. It is rebuilt from page frontmatter by bin/generate-index.py:

• Run python bin/generate-index.py (or python3) before reading the index, and after any operation that adds, removes, renames, or re-categorizes a page.
• The generator groups pages by their category frontmatter, in the order categories are listed under Index Categories below; within a category it lists pages newest-first by created. Each entry is - [[slug]] — summary _(created)_.
• Pages whose filename matches audit-*.md are excluded (gitignored local-only artifacts). A page with an unrecognized or missing category lands in an Uncategorized section.

Index Categories

<one per line, matching the user's chosen taxonomy>

Conventions

• raw/ is immutable — skills never modify it
• operation log: git wikis record each op as a commit (see Operation Log & Commit Convention) and render it with bin/render-log.py; non-git wikis append to log.md (append-only, never rewritten)
• index.md is GENERATED by bin/generate-index.py and is gitignored — never hand-edit it; set page frontmatter (category, summary) and regenerate instead
• All pages live flat in wiki/pages/ — no subdirectories
• overview.md reflects the current synthesis across all sources
• Cross-reference and citation slug-targets follow config/link-style.md — every skill reads it before writing or scanning links
• contradiction check: ingest gates on blocking contradictions in touched pages via a transient contradiction-check: failed flag, removed before commit — committed pages are always clean (see Contradiction Check)
• pre-commit gate: git wikis run bin/hooks/pre-commit (via core.hooksPath) → bin/check-contradictions.py, which blocks any commit staging a page that still carries the flag (see Pre-commit Gate); re-run git config core.hooksPath bin/hooks after a fresh clone

4. Install the bin/ helper scripts and generate the index

The wiki ships four stdlib-only helper scripts (no dependencies) plus a tracked git hook. They are bundled with this skill at assets/bin/ — copy them verbatim into <wiki-root>/bin/ (do not retype or regenerate them). From this skill's directory:

mkdir -p <wiki-root>/bin/hooks
cp assets/bin/generate-index.py       <wiki-root>/bin/
cp assets/bin/render-log.py           <wiki-root>/bin/
cp assets/bin/check-contradictions.py <wiki-root>/bin/
cp assets/bin/lint-mechanical.py      <wiki-root>/bin/
cp assets/bin/hooks/pre-commit        <wiki-root>/bin/hooks/
chmod +x <wiki-root>/bin/*.py <wiki-root>/bin/hooks/pre-commit

What each one does:

• bin/generate-index.py — wiki/index.md is generated from page frontmatter, never hand-written, so it can never drift from reality. After copying, run it once (python bin/generate-index.py) so a valid index.md exists.
• bin/render-log.py — renders the operation log from git history on demand (see the Operation Log & Commit Convention in SCHEMA.md). Harmless on a non-git wiki — it just reports that the log lives in log.md.
• bin/check-contradictions.py — a pre-commit gate (see the Pre-commit Gate and Contradiction Check sections in SCHEMA.md). It blocks a commit that stages a wiki/pages/ file still carrying P8's contradiction-check: failed flag. Deterministic, no LLM. Harmless on a non-git wiki — it no-ops.
• bin/lint-mechanical.py — the deterministic health checks, two modes. Full mode (python bin/lint-mechanical.py) emits JSON for wiki-lint's Phase 1 (broken links, orphans, missing frontmatter, slug collisions, stale-date, missing-concept) plus the tag-cluster list for its contradiction sweep. Staged mode (--staged) is the second pre-commit gate: it blocks a commit whose staged pages have missing frontmatter, a broken link, or a slug collision. No LLM; no-ops outside a git work tree.
• bin/hooks/pre-commit — the tracked git hook that chains both gates (check-contradictions.py, then lint-mechanical.py --staged) via uv run (so an interpreter is guaranteed). It is wired up in step 5.

5. Set up the operation log

How operations are logged depends on whether the wiki is a git repo. Offer to run git init if it isn't one already — the git-history log is the better path.

• Git repo: the git history is the operation log (see SCHEMA's Operation Log & Commit Convention). Do not create log.md. First install the pre-commit gates (contradiction flag + structural validity): make the hook executable and point git at the tracked hooks directory —

  chmod +x bin/hooks/pre-commit
  git config core.hooksPath bin/hooks
  

  The hook is tracked (committed below), but core.hooksPath is repo-local config that does not survive a fresh clone — tell the user to re-run the git config line after cloning. Then suggest the initial commit and make it on the user's confirmation:

  chore: initialize <domain> wiki
  
  Wiki-Op: init
  

• Not a git repo: create wiki/log.md as the fallback operation log:

  # Wiki Log
  
  Append-only fallback log (this wiki is not a git repo). Format:
  `## [YYYY-MM-DD] <operation> | <title>` — recent: `grep "^## \[" log.md | tail -10`
  
  ---
  
  ## [<today>] init | <domain>
  

6. Write wiki/overview.md

---
title: Overview
tags: [overview, synthesis]
sources: []
updated: <today>
---

# <Domain> — Overview

> Evolving synthesis of everything in the wiki. Updated by wiki-ingest when sources shift the understanding.

## Current Understanding

*No sources ingested yet.*

## Open Questions

*Add questions here as they arise.*

## Key Entities / Concepts

*Populated as pages are created.*

7. Confirm

Tell the user:

• Wiki initialized at <path>
• Link style: <obsidian | markdown> — see config/link-style.md for the rule. To switch later, replace that file with the other variant from this skill's config/ directory and update link_style: in SCHEMA.md. Existing pages will not be auto-converted.
• Add sources to raw/ manually, or run wiki-ingest directly with a URL or file path
• Run wiki-lint periodically to keep the wiki healthy
• For a git wiki, each operation is recorded as a commit; see the operation log with python bin/render-log.py
• SCHEMA.md is how all other skills locate this wiki — do not move or delete it