LLM Wiki — Graph Index Skill (wiki_graph_index)

Resolving script paths (read first): Commands below invoke scripts as <BIN>/X.py (and a few as <SKILLS>/...). Resolve these to absolute paths once before running anything:

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- <SKILL_DIR> = the directory this SKILL.md lives in. - <SKILLS> = the skills/ folder containing this skill = <SKILL_DIR>/.. - <BIN> = the bin/ folder beside it = <SKILL_DIR>/../../bin

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Do not hardcode a fixed prefix like .agents/bin or ../bin: shell relative paths resolve against the current working directory (usually the topic root), not this skill's location. Once resolved, <BIN> is typically .agents/bin when invoked from the hub root, or .claude/bin from inside a topic directory.

This skill extracts the Markdown-based knowledge graph (comprised of [[wikilinks]], tags, and aliases) into a structured SQLite database (output/graph.db) that an AI agent can easily query using standard SQL.

Usage

When the user asks to extract, index, or query the knowledge graph of their wiki:

1. Build the Graph Database

Run the deterministic python script to extract the graph from the markdown files:

python <BIN>/llm-wiki.py graph <TOPIC_DIR>

This will parse all markdown files under `wiki/` (ignoring `_index.md`), extract frontmatter (tags, aliases) and body links, and rebuild the SQLite database located at `output/graph.db`.

2. Query the Graph Database

Once built, you (the AI) can query output/graph.db using Python's sqlite3 module to traverse the graph and answer the user's questions.

The database schema is as follows:

• nodes(id, path, title, type, category, summary, created, updated)
• id: The file path without extension (e.g., 'concepts/concept_name') or a tag (e.g., 'tag:machine-learning').
• edges(source_id, target_id, type)
• type can be 'wikilink' (between files) or 'has_tag' (from file to tag node).
• tags(node_id, tag)
• aliases(node_id, alias)

Use python <BIN>/query-graph.py "<SQL>" --db <TOPIC_DIR>/output/graph.db to query the knowledge graph. Do not use direct sqlite3 command line execution.

Example:

python <BIN>/query-graph.py "SELECT source_id FROM edges WHERE target_id = 'Transformer';" --db <TOPIC_DIR>/output/graph.db

Or via a temporary Python script if you need complex graph traversal.

3. Report

Present the findings of your graph queries to the user.

Error Handling

• If any script exits with non-zero code, report the full stderr output to the user and stop.
• If a file cannot be read or parsed, log a warning and continue with remaining files.
• Do NOT silently skip errors or proceed with partial results without reporting.