[[ secondbrainos ]]

The full component tree

Everything in the repository on one page, annotated. Every line is a link: pages open on this site, code opens on GitHub. Click a branch to fold it.

README.md# Guide index, quickstart, curated catalog
CONTRIBUTING.md# Primary sources only, no affiliate links
LICENSE# MIT
agents/# 6 subagents, 4 of them read-only
curator.md# Proposes what to prune, archive or merge
graph-analyst.md# Analyses the link graph and reports metrics, hubs, bridges and clusters
ingestor.md# Processes new material in raw/ into linked wiki pages
linker.md# Finds and adds missing connections between existing wiki pages
researcher.md# Answers a research question from the vault and flags what is missing
reviewer.md# Produces the periodic review of what the vault learned
skills/# 18 skills, one per workflow
second-brain-backfill/# Import a large archive into the vault in controlled batches: triage wha…
second-brain-changed-my-mind/# Trace where the user's recorded position on something has shifted: supe…
second-brain-chat-import/# Triage an exported chat history into what to ingest, what to archive an…
second-brain-graph/# Analyse the vault's link graph and report on its shape: orphan rate, av…
second-brain-ingest/# Turn raw source material in a second-brain vault into linked wiki pages…
second-brain-lint/# Audit a second-brain vault for structural problems and repair them: bro…
second-brain-merge/# Merge two pages that describe the same thing, preserving every distinct…
second-brain-metrics/# Record a dated snapshot of the vault's health numbers and compare again…
second-brain-privacy/# Audit the vault for material that should not be in it: credentials, oth…
second-brain-project/# Set up or update a project in the vault: the four-stage folder pipeline…
second-brain-publish/# Prepare a subset of the vault for publishing: check opt-in flags, find …
second-brain-query/# Answer a question from a second-brain vault by reading its own pages, c…
second-brain-quiz/# Generate questions from the user's own concept pages so they can find o…
second-brain-rename/# Rename a page safely: update the file, fix every inbound wikilink, add …
second-brain-report/# Produce a research report from the vault: scope the question against ex…
second-brain-review/# Produce a periodic review of a second-brain vault: what was added, whic…
second-brain-transcript/# Clean a raw transcript before ingestion: punctuate, paragraph, label sp…
second-brain-write/# Draft from the vault: outline from concept pages, keep citations to the…
plugins/# the course's tools as a Claude Code plugin, installable in two commands
/agents-course:context-audit# Audit an agent's context layout against the four places: system prompt,…
/agents-course:evals-bootstrap# Scaffold a first eval suite for an agent: mine real failures into cases…
/agents-course:gate-check# Find the decisions in a pipeline that do not need the expensive model a…
/agents-course:goal-test# Turn a vague task into a testable definition of done and generate an ex…
/agents-course:harness-audit# Audit an agent's harness against the four rings: containment, guides, s…
agents-course:loop-critic# Reviews the result of an agent loop iteration in a clean context: check…
commands/# 72 slash commands, thin by design
ingestion/# 10
/ingest# Ingest new material from raw/ into the wiki
/ingest-url# Clip and ingest a web page
/ingest-youtube# Ingest a video or podcast transcript
/ingest-pdf# Ingest a PDF
/ingest-paper# Ingest an academic paper
/ingest-chats# Import an exported chat history
/ingest-voice# Ingest a voice note
/ingest-newsletter# Ingest newsletters without duplicating
/ingest-highlights# Ingest book or article highlights
/backfill# Bulk import an archive in batches
structuring/# 11
/link# Find and add missing connections
/dedupe# Find near-duplicate pages
/merge# Merge two pages
/rename# Rename a page and fix every link
/split# Split an overloaded page
/retype# Fix a page's type
/schema# Check frontmatter against the schema
/tags# Audit the tag vocabulary
/aliases# Find missing aliases
/contradictions# List unresolved contradictions
/index# Rebuild the index
graph/# 8
/graph# Report the shape of the graph
/graph-export# Export the graph for outside analysis
/orphans# Find unreachable pages
/hubs# Find pages that swallowed the graph
/bridges# Find the pages holding the graph together
/clusters# Show what the vault is actually about
/typed-links# Add relation types where they matter
/stale# Find concept pages nobody has touched
retrieval/# 10
/ask# Ask a question answered only from the vault
/know# What do I know about a topic
/connect# Find the path between two ideas
/compare# Compare two things from your own sources
/sources# Show what a claim rests on
/gaps# What is missing from my understanding
/contradicts# Argue against me
/timeline# How my sources developed over time
/trace# Show which pages an answer used
/changed-my-mind# What I have revised
maintenance/# 9
/lint# Audit structure and repair what is mechanical
/health# Quick health check
/metrics# Record a dated metrics snapshot
/review# Periodic review of what the vault learned
/weekly# The weekly review
/monthly# The monthly structural review
/prune# Find what is safe to remove
/archive# Move cold material out of the wiki
/commit# Commit the current state with a useful message
outputs/# 8
/outline# Outline a piece from your concept pages
/draft# Draft from the vault
/report# Write a research report
/publish# Check what is safe to publish
/export# Export a page or set of pages
/quiz# Test yourself on your own pages
/explain# Explain it back and find the gaps
/ingest-mine# Ingest your own finished work
projects/# 6
/project# Create a project
/project-status# Where a project stands
/decisions# List decisions made
/commitments# List open commitments
/handoff# Prepare a handoff brief
/scope# Pull knowledge into a project
safety/# 5
/privacy# Audit what should not be in the vault
/secrets# Scan for credentials
/dry-run# Preview a run without writing
/rollback# Undo the last run
/audit# Audit what an agent did
setup/# 5
/init# Scaffold a new vault
/claude-md# Build or update your CLAUDE.md
/install# Install the skills, commands and agents
/doctor# Check the setup is working
/schedule# Set up scheduled maintenance
scripts/# Dependency-free Python
build_tracks.py# Inject the compact topic tracks into index.html
build_tree.py# Generate tree.html - the full component tree as one interactive page
chat_export_to_md.py# Convert an exported chat history JSON into one markdown file per conver…
graph_export.py# Export a vault's wikilink graph as CSV edges or GraphML
link_check.py# Check a second-brain vault for broken wikilinks, orphan pages and stubs
vault_stats.py# Print health metrics for a second-brain vault
vault-template/# Clone this folder, open it in Obsidian, run /init
CLAUDE.md# Page contracts, linking rules, contradictions
raw/# Sources land here, never edited after
wiki/# The artefact the agent maintains
wiki/sources/# One page per ingested item
wiki/entities/# People, orgs, projects, tools
wiki/concepts/# Ideas. The pages that compound
wiki/synthesis/# Only when it says what no source did
wiki/index.md# Catalog. Read first, always
wiki/log.md# One line per run. Makes it auditable
projects/# Inputs / Process / Outputs / Feedback
templates/# Source, concept, entity, synthesis
output/# Reports and drafts, ingested back later
docs/# The guide. 10 sections, 65 pages
01-concepts/# Concepts · 8 pages
what-is-a-second-brain.md# What a second brain actually is
the-save-for-later-paradox.md# The save-for-later paradox
llm-wiki-pattern.md# The LLM wiki pattern
two-layers.md# The two layers
why-markdown-and-plain-text.md# Why markdown and plain text
pkm-lineage.md# Zettelkasten, PARA, evergreen notes
wiki-vs-rag.md# Wiki vs RAG
what-good-looks-like.md# What good looks like
02-setup/# Setup · 9 pages
obsidian-install-and-vault.md# Obsidian and your first vault
claude-code-setup.md# Claude Code in the vault
mcp-obsidian.md# MCP for Obsidian
claude-md.md# Writing your CLAUDE.md
vault-structure.md# Vault structure
project-scoping.md# Project scoping
live-data.md# Live data connectors
obsidian-plugins.md# Plugins worth installing
git-and-sync.md# Git, sync and backups
03-ingestion/# Ingestion · 7 pages
web-clipper.md# Web articles
youtube-transcripts.md# YouTube and podcasts
pdfs-and-books.md# PDFs, papers and books
chat-exports.md# Chat exports
voice-and-meetings.md# Voice notes and meetings
newsletters-and-email.md# Newsletters and email
bulk-backfill.md# Backfilling years of material
04-structuring/# Structuring · 8 pages
atomic-pages.md# One page, one idea
page-types.md# The four page types
linking-rules.md# Linking rules
frontmatter-schema.md# Frontmatter schema
naming-and-aliases.md# Naming and aliases
dedupe-and-merge.md# Deduplication and merging
contradictions-and-supersession.md# Contradictions and supersession
index-and-log.md# index.md and log.md
05-graphs/# Graphs · 7 pages
graph-basics.md# Graph basics for a knowledge base
obsidian-graph-view.md# Reading the Obsidian graph view
typed-links.md# Typed links
graph-vs-vectors.md# Graph vs embeddings
graphrag.md# GraphRAG and where it fits
exporting-your-graph.md# Exporting the graph
metrics.md# Graph metrics worth tracking
06-agents/# Agents · 6 pages
agent-roles.md# Agent roles
scheduled-maintenance.md# Scheduling
subagents.md# Subagents and parallel work
hooks.md# Hooks
skills-and-commands.md# Skills and slash commands
safety-and-guardrails.md# Guardrails
07-retrieval/# Retrieval · 5 pages
asking-questions.md# Asking the vault
query-patterns.md# Query patterns
search-tools.md# Search tools
rag-on-top.md# Adding RAG when you need it
context-budget.md# Context budget
08-outputs/# Outputs · 4 pages
writing-from-the-vault.md# Writing from the vault
research-reports.md# Research reports
publishing-and-export.md# Publishing and export
teaching-yourself.md# Learning from your own vault
09-maintenance/# Maintenance · 6 pages
lint-and-health.md# Linting the vault
review-cadence.md# Review cadence
versioning-with-git.md# Versioning
backups-and-portability.md# Backups and portability
privacy-and-secrets.md# Privacy
scaling.md# Scaling past a thousand pages
10-troubleshooting/# Troubleshooting · 5 pages
common-failures.md# The failures everyone hits
agent-writes-garbage.md# The agent writes garbage
broken-links.md# Broken links and orphans
vault-too-big.md# The vault got too big
faq.md# FAQ
docs/course-*/# The agents course. 7 modules, 21 pages
course-0-map/# 0 · The map · 3 pages
what-an-agent-is.md# What an agent is
five-layers.md# Five layers, one system
agents-or-workflows.md# Agents or workflows
course-1-context/# 1 · Context · 3 pages
how-models-read.md# How models read context
the-four-places.md# The four places
context-practice.md# Context in practice
course-2-loop/# 2 · Loop · 3 pages
loops-vs-workflows.md# Loops versus workflows
the-four-parts.md# The four parts of a loop
loop-practice.md# Loop practice: filter, loop, fall back
course-3-gate/# 3 · The gate · 3 pages
cheap-decisions.md# Cheap Decisions
gates-in-practice.md# Gates in Practice
gate-practice.md# Gate Practice
course-4-harness/# 4 · Harness · 3 pages
the-office.md# The Office
the-four-rings.md# The Four Rings
harness-practice.md# Harness Practice
course-5-evals/# 5 · Evals · 3 pages
two-kinds-of-checks.md# Two Kinds of Checks
judges-and-golden-sets.md# Judges and Golden Sets
evals-practice.md# Evals Practice
course-6-production/# 6 · Production · 3 pages
from-prototype.md# From Prototype to Production
operating-agents.md# Operating Agents
day-one-plan.md# The Day-One Plan
docs/track-*/# Five handbooks, 44 pages, each ends in a build
track-graph/# Knowledge graphs · 9 pages
why-graphs.md# Why Knowledge Graphs
graphrag.md# GraphRAG
building-graphs-with-llms.md# Building Graphs with LLMs
graph-stores.md# Graph Stores
tools.md# Tools
build-extract.md# Build: Extract the Graph
build-query.md# Build: Query It
build-use.md# Build: Put It in the Loop
resources.md# Resources
track-jev/# Jev engineering · 8 pages
system-one-models.md# System One Models
what-jev-is-good-for.md# What Jev Is Good For
jev-in-an-agent-stack.md# Jev in an Agent Stack
getting-started.md# Getting Started With Jev
build-decision-endpoint.md# Build: a Typed Decision Endpoint
build-router.md# Build: the Confidence-Gated Router
build-swap-in-jev.md# Build: the Jev Swap
resources.md# Jev Resources
track-harness/# Agent harnesses · 9 pages
what-a-harness-is.md# What a Harness Is
claude-code-as-harness.md# Claude Code as Harness
context-engineering.md# Context Engineering
tools-and-mcp.md# Tools and MCP
harness-landscape.md# Harness Landscape
build-the-loop.md# Build: the Loop
build-guardrails.md# Build: Permissions and Context
build-graduate.md# Build: Know When to Graduate
resources.md# Resources
track-loop/# Loop engineering · 9 pages
what-loop-engineering-is.md# What Loop Engineering Is
stop-conditions.md# Stop Conditions
critics-and-verification.md# Critics and Verification
context-hygiene.md# Context Hygiene
patterns.md# Patterns
build-goal-test.md# Build: the Goal Test
build-critic.md# Build: the Critic
build-overnight.md# Build: the Overnight Loop
resources.md# Resources
track-evals/# Eval engineering · 9 pages
why-evals.md# Why Evals
designing-evals.md# Designing Evals
llm-as-judge.md# LLM as Judge
agent-evals.md# Agent Evals
tooling.md# Eval Tooling
build-traces.md# Build: Read Your Traces
build-suite.md# Build: the Suite
build-ci.md# Build: the Gate
resources.md# Eval Resources
resources/# 88 vetted links, checked September 2026
papers.md# GraphRAG, HippoRAG, Lost in the Middle
plugins.md# Obsidian plugins ranked by installs
reading.md# Karpathy's gist, Ahrens, Forte, Matuschak
repos.md#
repositories.md# GraphRAG, agent memory, RAG frameworks
skills.md# More skills counted across the ecosystem
tools.md# Editors, capture, search, graph, publishing
18 skills · 72 commands · 6 subagents · 6 plugin tools · 6 scripts · 65 pages of guide · 21 course pages · 44 handbook pages · 88 vetted linksgenerated from the repo