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Obsidian Integration

Obsidian is optional but recommended. It turns your Memex workspace into a live visual knowledge graph where every [[wikilink]] becomes a navigable connection.

Setup

  1. Open Obsidian
  2. Click Open folder as vault (home screen, or File → Open Vault)
  3. Navigate to your Memex workspace directory and select it
  4. Obsidian indexes all .md files automatically - no configuration needed

Every [[wikilink]] in the files immediately becomes a live, clickable edge in the graph.

If Obsidian asks about trusting the vault, say yes. If it offers to create a .obsidian config folder inside your directory, allow it - this stores your graph settings and theme preferences. It doesn't affect how Claude reads the files, and the wikilink scan skips it automatically.

Graph View

Press Cmd+G (Mac) or Ctrl+G (Windows). Every .md file appears as a node; every [[link]] appears as an edge.

What you'll see:

  • _MANIFEST.md - the most-connected node; it links to every domain hub
  • Hub index files - mid-size nodes at the center of each domain cluster
  • memory/ files - dense cluster, all cross-linked
  • working/scratch/ideas.md - connected to memory cluster via session-start reads
  • Tier 3 archived files - sparse, isolated at the edges (this is correct - they're not linked from active files)
  • Ghost files - if Obsidian auto-created any 0-byte .md stubs by clicking an unresolved link, they'll appear as orphaned nodes. Delete them (right-click → Move to Trash) or in Finder.

Color Groups

In Graph View, click the gear icon (top-left of the panel) → Groups. Add one group per folder. First match wins, so order matters - put more specific paths before broader ones.

Example groups:

Group name Filter Suggested color
Memory path:memory/ Gold / amber
Scratch path:working/scratch/ Gray
[Domain 1] path:working/[domain-1]/ Blue
[Domain 2] path:working/[domain-2]/ Purple
[Domain 3] path:working/[domain-3]/ Teal
[Domain 4] path:working/[domain-4]/ Green
Root path: White

Color choice is personal preference. The goal is that each domain reads as a visually distinct cluster at a glance.

Navigation Shortcuts

Action Shortcut
Open any file by name Cmd+O
Full-text search Cmd+Shift+F
Toggle graph view Cmd+G
See what links to current file Right panel → Backlinks
See all outgoing links Right panel → Outgoing links
Follow a wikilink Cmd+click

Keeping Obsidian and Claude in Sync

  • Rename files in Finder or via Claude, not inside Obsidian. Obsidian will try to update links it knows about, but Claude won't know the rename happened until the next wikilink scan. Use the session-end skill to catch drift.
  • Don't click unresolved links in Obsidian. Clicking a dotted (unresolved) link creates a blank stub file. This pollutes the workspace with empty files. If you see dotted links, run /memex:wikilinks to find the source and fix it.
  • No pipe aliases in table cells. [[name|display text]] inside a Markdown table breaks table rendering. Pipe aliases are fine in regular prose.
  • The .obsidian/ folder is safe to ignore. Claude's wikilink scan skips all hidden folders. Don't delete .obsidian/ - it stores your graph groups, theme, and settings.