knowledge-base

Cogito, ergo sum

Overview

This repository serves as my personal digital garden — a collection of interconnected notes, learnings, and insights gathered throughout my professional journey. It follows a Zettelkasten-style note-taking approach, where knowledge is organized in an organic, networked structure rather than a rigid hierarchy.

The vault is also indexed as a graphify knowledge graph and exposed to Claude Code as an MCP server, so the notes can be queried by any Claude Code session (in this repo or others) with source-cited retrieval.

Topics covered:

• Software Engineering
• Data Science
• Management & Leadership
• Productivity
• Health & Wellness
• Design
• And more...

Structure

• /Permanent/ — long-form, well-developed notes
• /software-engineer/ — technical notes on software development
• /data-science/ — data science, machine learning, and analytics
• /management/ — leadership and management insights
• /productivity/ — personal effectiveness techniques
• /health/ — health and wellness
• /design/ — design principles and practices
• /random-thoughts/ — daily thoughts and quick captures
• /Readwise/ — imported highlights and articles from Readwise
• /meetup/, /LaTex/, /content/, /assets/ — supporting material
• /graphify-out/ — generated knowledge graph (graph.json), rebuilt by /graphify

Claude Code + MCP setup

One-time

The graphify pipx venv needs the mcp module:

pipx inject graphifyy mcp

Then (re)build the graph:

/graphify .

Usage in this repo

Starting Claude Code from this directory auto-loads .mcp.json, giving any agent in the session access to the graphify MCP server (query_graph, get_node, get_neighbors, get_community, god_nodes, graph_stats, shortest_path).

• /kb <question> — retrieves relevant notes with citations via the kb-retriever subagent.
• /graphify — rebuilds the graph; /graphify --update re-extracts only changed files.
• Editing a .md file marks the graph stale (graphify-out/.needs_update) and prints a one-line hint.

Using this KB from another project

Add a graphify MCP entry to that project's .mcp.json:

{
  "mcpServers": {
    "kb": {
      "type": "stdio",
      "command": "/path/to/knowledge-base/scripts/kb-serve.sh",
      "env": {
        "KB_GRAPH_PATH": "/path/to/knowledge-base/graphify-out/graph.json"
      }
    }
  }
}

KB_GRAPH_PATH makes the launcher serve this KB's graph regardless of where the caller session started. In agent-flow orchestrations, Riko / Senku / Lawliet already have mcp__graphify__* in their allowed tools and will pick it up automatically.

Key files

• .mcp.json — declares the graphify MCP server for this repo
• scripts/kb-serve.sh — portable launcher (honors KB_GRAPH_PATH)
• .claude/commands/kb.md — /kb slash command
• .claude/agents/kb-retriever.md — retrieval subagent with citation formatting
• .claude/hooks/hooks.json + mark-graph-stale.sh — post-edit stale marker
• graphify-out/graph.json — the knowledge graph

How to browse manually

• Notes are plain Markdown — open any folder that matches your interest.
• Links between notes form a network; follow them to explore related ideas.
• Recent Notes.md is a running index of the latest entries.