Chain

Orchestrate the complete knowledge pipeline — self-learn, ingest, audit, absorb, and sync — in a single automated command.

/chain runs every step of the Brain OS knowledge pipeline in sequence, from raw epub to a committed, synced vault. Use it when you want to process a new book end-to-end without manually triggering each skill.

Each step must complete successfully before the next one starts. Do not skip steps — the pipeline is designed so each step depends on the output of the previous one.

Usage

# Full pipeline for a new book
/chain <epub_path> --notebook-id <nlm_id>

# Resume a pipeline that was interrupted
/chain --resume

# Show pipeline status for all books
/chain --status

Pipeline Steps

1. /self-learn — Extract, validate, extend

   Runs all three phases autonomously:

   • Phase 1 (Extract): Parses the epub and writes atomic concept notes to knowledge/raw/
   • Phase 2 (Validate): Runs the 4-role autoresearch loop against NotebookLM, repeating until 100% of questions pass at ≥95
   • Phase 3 (Extend): Writes synthesis, applied domain, and research extension notes

   Phase 2 has no timeout — it loops until mastery is achieved.

2. /ingest — Raw notes to structured book note

   Converts the raw extracted notes into a single structured book note at {vault}/knowledge/books/[book-slug].md using the Book Note Template, then updates the books index.

3. /audit — 50 fresh questions vs NotebookLM

   Runs an independent verification pass with 50 new questions (25 topic, 15 cross-cutting, 10 adversarial). If 100% pass at ≥95, the audit flag is set to true. If any fail, the pipeline stops and a task is written to your inbox.

4. /absorb — Connect insights to your vault

   Because the audit flag is already true, /absorb bypasses the approval prompt and applies vault connections automatically — updating your strategy, goals, and thinking notes based on the book’s insights.

5. /sync — Commit and push

   Commits all vault changes and pushes to your configured git remote.

6. Notify — Inbox, daily note, flag timestamp

   Updates all 3 notification channels:

   • Adds a review task to business/tasks/inbox.md
   • Creates or updates the daily note with a pipeline completion log
   • Writes a pipeline_completed timestamp to the audit flag file

Pipeline State

Each book’s pipeline state is tracked in _validation/audit-flag.json:

{
  "flag": "true|false|manual",
  "last_audit": "ISO timestamp",
  "audit_score": "159/159 at >=95",
  "pipeline_completed": "ISO timestamp",
  "ingested": true,
  "absorbed": true
}

/chain --resume reads this file to determine which step to continue from after an interruption.

Error Handling

Phase 2 fails (< 100% pass rate)

The validation loop continues indefinitely — there is no timeout. It generates new questions targeting weak topics and keeps iterating until every question passes at ≥95. The pipeline only proceeds to /ingest once 100% pass rate is achieved.

Audit fails

The pipeline stops immediately. The audit flag stays false. A task is written to business/tasks/inbox.md with details about which questions failed. Run /audit manually after reviewing and correcting your notes, then use /chain --resume to continue.

Git push fails

Pull the latest changes first to reconcile any remote updates, resolve any conflicts, then retry the push. /chain --resume will restart from the sync step.

NotebookLM timeout

The skill retries 3 times with exponential backoff. If all 3 retries fail, the pipeline pauses and notifies you to check your NotebookLM connection before resuming.