Command reference

Every command, flag, and example for the wiki CLI.

wiki init

Scaffold a new wiki project. Creates the directory structure, a schema.md behavioral spec, and starter index.md and log.md files.

wiki init <path> [--name NAME]

Flag	Description
`--name, -n`	Human-readable name for the wiki. Used in index and log headings.

Examples:

wiki init my-research/
wiki init my-research/ --name "ML Paper Notes"

wiki ingest

Read a source document and integrate it into the wiki. The LLM writes a source summary page, creates or updates concept and entity pages, refreshes index.md, and appends an entry to log.md.

wiki ingest <source> [flags]

Flag	Description
`--wiki, -w`	Override the wiki root directory. Defaults to auto-discovery (walks up from current directory looking for `schema.md`).
`--provider, -p`	LLM provider: `anthropic` or `openai`.
`--model, -m`	Model name override, e.g. `claude-sonnet-4-6` or `gpt-4o-mini`.
`--thinking`	Show the model's extended reasoning steps (Anthropic only).
`--delete-pdf`	Delete the original PDF after converting to text.

Examples:

# Ingest a markdown file
wiki ingest raw/paper.md

# Use OpenAI with a cheaper model
wiki ingest raw/article.md --provider openai --model gpt-4o-mini

# Ingest a PDF (requires pdftotext)
wiki ingest raw/paper.pdf --delete-pdf

# Show the model's reasoning
wiki ingest raw/notes.md --thinking

Supported formats: .md, .txt, .rst, and other plain text files. PDFs are auto-converted to text when pdftotext is installed.

wiki query

Ask a question against the wiki. The LLM reads index.md to find relevant pages, reads those pages, and synthesizes an answer. With --save, the answer is filed back into the wiki as a new concept page.

wiki query "<question>" [flags]

Flag	Description
`--wiki, -w`	Override wiki root directory.
`--save, -s`	Save the answer back into the wiki as a new concept page.
`--format, -f`	Output format: `markdown` (default), `table`, or `marp` (slide deck).
`--output, -o`	Write the answer to a file instead of printing to stdout.
`--provider, -p`	LLM provider override.
`--model, -m`	Model name override.
`--thinking`	Show extended reasoning steps (Anthropic only).

Examples:

# Basic query
wiki query "what is the transformer architecture?"

# Get a comparison table
wiki query "compare attention mechanisms across these papers" --format table

# Save a good answer back into the wiki
wiki query "summarize everything I know about RLHF" --save

# Write to a file
wiki query "what are the key open problems?" --output open-problems.md

# Generate a Marp slide deck
wiki query "give me a presentation on self-attention" --format marp --output slides.md

Tip: Use --save on high-quality queries. Answers filed back into the wiki become reusable knowledge that improves future queries.

wiki lint

Run a health check across the wiki. The LLM reads all pages and reports issues. With --fix, it repairs them automatically.

wiki lint [flags]

Flag	Description
`--wiki, -w`	Override wiki root directory.
`--fix`	Automatically fix issues instead of just reporting them.
`--provider, -p`	LLM provider override.
`--model, -m`	Model name override.
`--thinking`	Show extended reasoning steps (Anthropic only).

What lint checks for:

Orphan pages — pages with no inbound links from other wiki pages.
Missing cross-references — entities or concepts mentioned in pages but not linked.
Contradictions — conflicting claims across different pages.
Stale or vague claims — assertions that should be updated or clarified.
Concepts without their own page — ideas mentioned across multiple pages that deserve a dedicated page.
Outdated index.md entries — pages that exist but aren't listed, or listed but don't exist.

Examples:

# Report only
wiki lint

# Auto-fix issues
wiki lint --fix

wiki status

Show a summary of the wiki — page counts by type, raw file count, total word count. Does not call the LLM.

wiki status [--wiki PATH]

Example output:

Wiki: AI Research
  Sources:   12
  Concepts:  34
  Entities:  18
  Raw files:  12
  Words:     24,310

wiki config

Manage provider, model, and API key settings. Saved to ~/.wiki-builder/config.json.

wiki config [flags]

Flag	Description
`--provider`	Set the default provider: `anthropic` or `openai`.
`--api-key`	Save the API key for the selected provider.
`--model`	Set the default model name.
`--show`	Print the current configuration.

Examples:

# Set Anthropic as default
wiki config --provider anthropic --api-key sk-ant-...

# Switch to OpenAI
wiki config --provider openai --api-key sk-...

# Use a specific model by default
wiki config --model claude-sonnet-4-6

# Show current config
wiki config --show

Next: Providers & models