knowledge-ingest

Populate or update agent-knowledge from a codebase. Tree-sitter extracts structure (zero LLM tokens), then the agent distills clusters into knowledge entries + graph edges via existing MCP tools.

First run: full ingest — scans all files, creates entries from scratch. Subsequent runs: incremental — only reprocesses files whose SHA256 changed, adds entries for new files, removes entries for deleted files. The .knowledge-ingest-cache.json file in the target directory tracks state between runs.

When to use

• Onboarding a new project — bootstrap the knowledge base so future sessions have context
• After a refactor — re-run to update subsystem boundaries and relationships
• Periodic refresh — re-run after significant changes to keep knowledge current
• Importing documentation — PDFs, architecture diagrams, or external URLs

When NOT to use

• Single-file changes — just write a knowledge entry manually
• No code changes since last ingest — the cache will skip everything anyway (fast no-op)

Procedure

Phase 0 — Validation

1. Confirm the target path exists and is a directory.
2. Detect project name:

• Check package.json → name field
• Check Cargo.toml → [package] name
• Check go.mod → module line
• Check pyproject.toml → [project] name
• Fall back to directory basename

1. Check for .knowledge-ingest-cache.json in the target directory. If found, load it — this is an incremental run. Report how many files changed since last ingest.

Phase 1 — Structural Extraction (zero tokens)

1. Locate the tree-sitter extraction script. It ships with agent-knowledge:

node "<agent-knowledge-repo>/scripts/tree-sitter-extract.mjs" "<target-path>" --exclude "node_modules,dist,.git,vendor,__pycache__,build,target,.venv,coverage" --json

To find <agent-knowledge-repo>, check common locations:

• ~/.claude/mcp-servers/agent-knowledge/
• Or locate via: dirname $(which agent-knowledge)/../

1. Capture the JSON output. It contains per-file: symbols (classes, functions, methods), imports, exports, rationale comments (WHY/NOTE/DECISION/HACK/TODO/FIXME), call edges, SHA256 hashes, and a dependency graph.

1. If the script fails (missing dependency, path error), report the error to the user and offer to fall back to manual file reading for a subset of key files.

Phase 2 — Clustering

1. From the dependency graph and directory structure, group files into subsystems:

• Files that import each other heavily belong to the same cluster
• Files in the same directory with related names belong to the same cluster
• Entry points (files with no importers) get flagged as roots
• Aim for 5-30 clusters. If more, merge the smallest.
• Name each cluster from its directory name or dominant class/module.

1. Identify structural highlights:

• God nodes: symbols imported by 5+ files
• Entry points: files not imported by anything (CLI entry, main, index)
• Cross-cutting concerns: symbols used across multiple clusters

Phase 3 — Knowledge Entry Creation

1. Create the project overview entry:

knowledge({ action: "write", category: "projects", filename: "<project-name>", content: "---\ntitle: <Project Name>\ntags: [auto-ingested, <primary-language>]\nupdated: <today>\nconfidence: inferred\nconfidence_score: 0.8\n---\n\n# <Project Name>\n\n## Tech Stack\n...\n\n## Architecture\n...\n\n## Entry Points\n...\n\n## Subsystems\n- <cluster-1>: <one-line description>\n- <cluster-2>: <one-line description>\n..." })

Include: project name, tech stack (languages, frameworks, key dependencies), directory structure overview, entry points, subsystem list with one-line descriptions.

1. For each cluster/subsystem, create a subsystem entry:

knowledge({ action: "write", category: "notes", filename: "<project>-<cluster-name>", content: "---\ntitle: <Project> — <Cluster Name>\ntags: [auto-ingested, subsystem, <language>]\nupdated: <today>\nconfidence: inferred\nconfidence_score: 0.75\n---\n\n## Purpose\n<inferred from symbol names and structure>\n\n## Key Symbols\n- `ClassName` (line N) — <from docstring or inferred>\n- `functionName(params)` (line N)\n\n## Dependencies\nImports from: <other clusters>\nImported by: <other clusters>\n\n## Rationale\n<any WHY/NOTE/DECISION comments found in this cluster>" })

Keep each entry under 300 words. Focus on structure and relationships, not implementation details.

1. For rationale comments (WHY/DECISION/HACK), create decision entries:

knowledge({ action: "write", category: "decisions", filename: "<project>-<slug>", content: "---\ntitle: <Decision summary>\ntags: [auto-ingested, rationale]\nupdated: <today>\nconfidence: extracted\nconfidence_score: 1.0\n---\n\n## Decision\n<the rationale comment text>\n\n## Context\nFile: `<file-path>`, line <N>\nSymbol: `<enclosing function/class>`\n\n## Related\n<other rationale comments or subsystems this connects to>" })

Only create decision entries for substantive rationale (WHY, DECISION, SAFETY). Skip generic TODOs and FIXMEs unless they contain real architectural reasoning.

1. For CI/build configs found in the project (.github/workflows/, Makefile, Dockerfile, docker-compose.yml, Jenkinsfile, .gitlab-ci.yml), read them directly and create workflow entries:

knowledge({ action: "write", category: "workflows", filename: "<project>-<workflow>", content: "..." })

Summarize: what the workflow does, triggers, key steps, deployment targets.

Phase 4 — Graph Edges

1. Create part_of edges from each subsystem to the project:

knowledge_graph({ action: "link", source: "notes/<project>-<cluster>.md", target: "projects/<project>.md", rel_type: "part_of", strength: 0.9, origin: "ingest" })

1. Create depends_on edges between subsystems based on the import dependency graph:

knowledge_graph({ action: "link", source: "notes/<project>-<cluster-a>.md", target: "notes/<project>-<cluster-b>.md", rel_type: "depends_on", strength: 0.8, origin: "ingest" })

1. Create builds_on edges from decisions to the subsystem they relate to:

knowledge_graph({ action: "link", source: "decisions/<project>-<decision>.md", target: "notes/<project>-<cluster>.md", rel_type: "builds_on", strength: 0.7, origin: "ingest" })

1. Do NOT manually create related_to edges — auto-linking fires on every knowledge write and handles cross-entry similarity.

Phase 5 — Multi-modal (if applicable)

1. If PDF files exist in the project (root, docs/, papers/):

• Read them natively (agent is multimodal)
• Write a summary entry to notes/<project>-<pdf-name>.md

1. If architecture diagram images exist (.png, .svg, .jpg in docs/, architecture/, diagrams/):

• Read them natively
• Write a description entry to notes/<project>-<diagram-name>.md

1. If URLs are provided by the user:

• Fetch via WebFetch
• Write summary entries to notes/

1. Skip this phase entirely if no such files exist. Do not search exhaustively for media files.

Phase 6 — Cache

1. Write .knowledge-ingest-cache.json to the target directory:

{
  "version": 1,
  "timestamp": "<ISO date>",
  "project": "<project-name>",
  "agent_knowledge_version": "<version>",
  "files": {
    "src/foo.ts": {
      "sha256": "abc123...",
      "entries": ["notes/<project>-foo-module.md"]
    }
  },
  "entries_created": [
    "projects/<project>.md",
    "notes/<project>-core.md",
    "decisions/<project>-auth-design.md"
  ]
}

1. On incremental re-runs, compare SHA256 hashes:

• Unchanged files: skip entirely
• Changed files: re-extract, update corresponding entries
• Deleted files: remove their entries from knowledge base via knowledge({ action: "delete" })
• New files: process normally

Phase 7 — Validate

1. Run the validation script to verify the ingest produced correct results:

node "<agent-knowledge-repo>/skills/knowledge-ingest/scripts/validate.mjs" "<target-path>"

1. Parse the JSON output. If status is FAIL:

• Review each issue in the issues array
• Fix the issue (create missing entries, repair the cache file, etc.)
• Re-run validation until it passes
• Only proceed to the report once validation passes

Phase 8 — Report

1. Print a summary:

Ingested <project-name>:
  Files scanned: N
  Clusters identified: N
  Entries created:
    - projects/: 1
    - notes/: N (subsystems)
    - decisions/: N (rationale)
    - workflows/: N (CI/build)
  Graph edges: N
  Skipped (cached): N files unchanged

Anti-patterns

• Do NOT read every file — that defeats the purpose of tree-sitter extraction. Only read files the agent needs for summarization (CI configs, READMEs, a few key entry points).
• Do NOT create one entry per file — cluster into subsystems. A 200-file project should produce ~15-25 entries, not 200.
• Do NOT skip the cache write — it is essential for incremental updates.
• Do NOT create `related_to` edges manually — auto-linking handles this on every write.
• Do NOT exceed 40 `knowledge write` calls in a single run — batch small clusters together if needed.
• Do NOT include raw source code in knowledge entries — focus on structure, purpose, and relationships.

Examples

/knowledge-ingest .
/knowledge-ingest ~/projects/my-api
/knowledge-ingest ./libs/auth --exclude "test,mock"