/understand-knowledge

Analyzes a Karpathy-pattern LLM wiki — a three-layer knowledge base with raw sources, wiki markdown, and a schema file — and produces an interactive knowledge graph dashboard.

What It Detects

The Karpathy LLM wiki pattern (see https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f):

• Raw sources — immutable source documents (articles, papers, data files)
• Wiki — LLM-generated markdown files with wikilinks ([[target]] syntax)
• Schema — CLAUDE.md, AGENTS.md, or similar configuration file
• index.md — content catalog organized by categories
• log.md — chronological operation log

Detection signals: has index.md + multiple .md files with wikilinks. May have raw/ directory and schema file.

Instructions

Phase 1: DETECT

1. Determine the target directory:

   • If the user provided a path argument, use that
   • Otherwise, use the current working directory

2. Run the format detection script bundled with this skill:

   python3 <SKILL_DIR>/parse-knowledge-base.py <TARGET_DIR>

   • If the script exits with an error, tell the user this doesn't appear to be a Karpathy-pattern wiki and explain what was expected
   • If successful, proceed. The script writes scan-manifest.json to <TARGET_DIR>/.understand-anything/intermediate/

3. Read the scan-manifest.json and announce the results:

   • "Detected Karpathy wiki: N articles, N sources, N topics, N wikilinks (N unresolved)"
   • List the categories found from index.md

Phase 2: SCAN (already done)

The parse script in Phase 1 already performed the deterministic scan. The scan-manifest.json contains:

• Article nodes (one per wiki .md file) with extracted wikilinks, headings, frontmatter
• Source nodes (one per raw/ file)
• Topic nodes (from index.md section headings)
• related edges (from wikilinks)
• categorized_under edges (from index.md sections)

No additional scanning is needed. Proceed to Phase 3.

Phase 3: ANALYZE

Dispatch article-analyzer subagents to extract implicit knowledge:

1. Read the scan-manifest.json to get the article list

2. Prepare batches of 10-15 articles each, grouped by category when possible (articles in the same category are more likely to have implicit cross-references)

3. For each batch, dispatch an article-analyzer subagent with:

   • The batch of articles (id, name, summary, wikilinks, category, content from knowledgeMeta)
   • The full list of existing node IDs (so the agent can reference them)
   • The batch number for output file naming
   • The intermediate directory path: $INTERMEDIATE_DIR = <TARGET_DIR>/.understand-anything/intermediate

   The agent will write analysis-batch-{N}.json to the intermediate directory.

4. Run up to 3 batches concurrently. Wait for all batches to complete.

5. If any batch fails, log a warning but continue — the scan-manifest provides a solid base graph even without LLM analysis.

Phase 4: MERGE

1. Run the merge script bundled with this skill:

   python3 <SKILL_DIR>/merge-knowledge-graph.py <TARGET_DIR>

2. The script:

   • Combines scan-manifest.json + all analysis-batch-*.json files
   • Deduplicates entities (case-insensitive name matching)
   • Normalizes node/edge types via alias maps
   • Builds layers from index.md categories
   • Builds a tour from index.md section ordering
   • Writes assembled-graph.json to the intermediate directory

3. Read the merge report from stderr and announce:

   • Total nodes, edges, layers, tour steps
   • How many entities/claims the LLM analysis added

Phase 5: SAVE

1. Read the assembled-graph.json

2. Run basic validation:

   • Every edge source/target must reference an existing node
   • Every node must have: id, type, name, summary, tags, complexity
   • Remove any edges with dangling references

3. Copy the validated graph to <TARGET_DIR>/.understand-anything/knowledge-graph.json

4. Write metadata to <TARGET_DIR>/.understand-anything/meta.json:

   {
     "lastAnalyzedAt": "<ISO timestamp>",
     "gitCommitHash": "<from git rev-parse HEAD or empty>",
     "version": "1.0.0",
     "analyzedFiles": <number of wiki articles>
   }

5. Clean up intermediate files:

   rm -rf <TARGET_DIR>/.understand-anything/intermediate

6. Report summary to the user:

   • "Knowledge graph saved: N articles, N entities, N topics, N claims, N sources"
   • "N edges (N wikilink, N categorized, N implicit)"
   • "N layers, N tour steps"

7. Auto-trigger the dashboard:

   /understand-dashboard <TARGET_DIR>

Notes

• The parse script handles ALL deterministic extraction (wikilinks, headings, frontmatter, categories from index.md). The LLM agents only add implicit knowledge that requires inference.
• Categories and taxonomy come from index.md section headings, NOT from filename prefixes. The Karpathy spec is intentionally abstract about naming conventions.
• The graph uses kind: "knowledge" to signal the dashboard to use force-directed layout instead of hierarchical dagre.
• Source nodes from raw/ are lightweight (filename + size only) — we don't parse PDFs or binary files.