GRAPH setup pack: Graphify + Obsidian + Claude Code

What you get: Claude Code reads a pile of docs, Graphify turns them into a knowledge graph, and Obsidian opens it as a linked vault. My run: 140 Claude Code doc pages → 1,932 ideas, 7,480 connections, 78 topic groups, 2,007 notes, about 20 minutes.

1. Install (one time)

• Claude Code: https://code.claude.com
• Obsidian (free): https://obsidian.md
• Graphify: https://github.com/Graphify-Labs/graphify
• uv tool install graphifyy (the package name has two y's)
• graphify install --platform claude (adds the /graphify skill to Claude Code)

2. The one-sentence prompt

Open Claude Code in an empty folder and paste:

download the official claude code docs, map them with /graphify, then turn that into an obsidian vault with --obsidian

Swap "the official claude code docs" for any docs you want: a library, your company wiki export, a folder of PDFs.

Good to know: if the pile is big (my download was 228 pages), Claude Code stops and asks how much to map. Pick a smaller scope first; extraction uses a lot of tokens (about 1.66M for my 140 pages, on a Claude plan).

3. Commands I used

• /graphify ./docs --obsidian (inside Claude Code: graph + Obsidian vault)
• /graphify ./docs --obsidian --obsidian-dir ~/vaults/my-project (write the vault into a folder you choose)
• graphify query "what do permission rules connect to?" (ask the graph from the terminal)
• graphify path "A" "B" (shortest path between two ideas)
• graphify explain "X" (plain-language summary of one idea and its neighbors)

Output lands in graphify-out/: graph.html (interactive map), GRAPH_REPORT.md, graph.json, and obsidian/ (the vault).

4. Where should the vault live? (pick one)

1. Its own vault: Obsidian → Open folder as vault → pick graphify-out/obsidian. (What I did. Hate it? Delete one folder.)
2. One folder inside your main vault that you can delete anytime.
3. Write straight into your main vault with --obsidian-dir.
4. Copy over only the notes you want.

5. Add links back to the source

In my run, the vault notes had no link to the original page. Claude Code noticed and added a source_url to each note. If yours don't have one, ask:

add a source_url to every note's frontmatter, built from its source_file

6. Use it

Open the vault in Obsidian → Graph view to see the map. Point Claude Code at the vault folder, and it can follow the links between ideas instead of searching page by page.