second-brain

A graph-based note and research system that finds related ideas across stored knowledge. It can expand a topic through nearby connections, identify areas to learn, and suggest possible links between notes.

In plain words
What is it for?
Use it to enrich research with connected notes, choose what to study next, or review and add well-supported links between ideas.
Why use it?
It helps uncover useful relationships and gaps that a simple keyword search may miss.

Skill for Claude CodeCodex

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

agentmods
npx agentmods add skills/grburgess/mindgap/second-brain
Any agent
npx skills add grburgess/mindgap --skill second-brain
Clone the repo
git clone --depth 1 https://github.com/grburgess/mindgap

Made for: Claude Code, Codex.

Per session 100 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 583 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. Scan, not verified.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5 $0.00100 $0.00583
Opus 5 $0.00050 $0.00292
Sonnet 5 $0.00020 $0.00117
Haiku 4.5 $0.00010 $0.00058

Measured yesterday against content hash 78901ff69717, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

second-brain scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured yesterday.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

mindgap-plugin/skills/second-brain/SKILL.md · 36 lines

What it actually says

second-brain

The graph has an analytic layer (mindgap mine / mindgap_mine_*) on top of plain retrieval. Math proposes cheap candidates; you adjudicate. Read AGENTS.md first for the ingest rules. mentions=0.25 is hygiene, not the precision lever.

Pick the mode by intent

  • enrich — grounding a topic you're working on. mindgap_mine_enrich(seed) returns the RWR-ranked relevant subgraph (reaches 2-3 hops, unlike 1-hop context). Read-only.
  • learn — deciding what to study/ingest next. mindgap_mine_learn() ranks the thin spots (stubs, isolated/fresh-thin papers, in-demand-thin concepts) and writes frontier.json for the {{TOPICS}} loops. Read-only.
  • connect — growing the graph with latent links. mindgap_mine_connect(k) returns guarded candidate pairs + both bodies + shared support. Gated write-back (below).

connect adjudication rubric (math proposes, you dispose)

For each candidate, read both bodies. Accept only if you can state the specific relationship in one sentence from the bodies — a nameable relationship, not mere co-occurrence. Otherwise reject. Per accepted pair choose rel (relates_to default; depends_on/implements/cites/part_of/ defines when the bodies justify it) and set confidence (0.5–0.8 for a new unverified link).

Gated write-back

Never raw-insert. Write confirmed links via mindgap_ingest with created_by="mine:connect". For a genuinely distant accepted pair (the candidate's distant flag), also synthesize a bridging insight node (type=concept, created_by=mine:connect, body = the one-line rationale with [[a]] [[b]] wiki-links). Show the batch before committing. Re-running is idempotent — already-linked pairs are skipped. (CLI equivalent: mindgap mine connect --apply decisions.json.)

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. yesterday First seen · 36 lines · 0 tokens per session scan A 78901ff69717

Subscribe to this mod's changes

second-brain is a skill published in the GitHub repository grburgess/mindgap (0 stars, last pushed 1mo ago), licensed MIT. It adds 100 tokens to every session and 583 once invoked, about $0.0005 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

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