feat: ship workspace.json + setup-vault.sh for zero-config user experience

Users who clone the repo now get the full setup automatically:

- workspace.json tracked in git (removed from .gitignore)
  - Opens with Wiki Map canvas as default view
  - Graph view pre-configured: path:wiki filter, 5 color groups, proper physics
  - Obsidian reads this on first open before any state reset occurs

- bin/setup-vault.sh — one-time setup script
  - Writes correct graph.json (filter + colors)
  - Writes app.json (excludes plugin dirs from graph)
  - Writes appearance.json (enables vault-colors CSS)
  - Prints clear next-step instructions
  - Usage: bash bin/setup-vault.sh

- README updated: Option 1 now shows clone + setup.sh as recommended path
  - Clear explanation of what the script does
  - 2-minute setup flow vs manual configuration

Result: users clone, run setup.sh, open Obsidian — done.
Graph shows only wiki pages, color-coded, no noise.

bin/setup-vault.sh

@@ -0,0 +1,85 @@
+#!/usr/bin/env bash
+# cosmic-brain vault setup script
+# Run this ONCE before opening Obsidian for the first time.
+# Usage: bash bin/setup-vault.sh [optional: /path/to/vault]
+# Default: uses the directory where this script lives (the vault root)
+
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+VAULT="${1:-$(dirname "$SCRIPT_DIR")}"
+OBSIDIAN="$VAULT/.obsidian"
+
+echo "Setting up cosmic-brain vault at: $VAULT"
+
+# ── 1. Create directories ─────────────────────────────────────────────────────
+mkdir -p "$OBSIDIAN/snippets"
+mkdir -p "$VAULT/.raw"
+mkdir -p "$VAULT/wiki/concepts" "$VAULT/wiki/entities" "$VAULT/wiki/sources" "$VAULT/wiki/meta"
+mkdir -p "$VAULT/_templates"
+
+# ── 2. Write graph.json ───────────────────────────────────────────────────────
+cat > "$OBSIDIAN/graph.json" << 'EOF'
+{
+  "collapse-filter": false,
+  "search": "path:wiki",
+  "showTags": false,
+  "showAttachments": false,
+  "hideUnresolved": true,
+  "showOrphans": false,
+  "collapse-color-groups": false,
+  "colorGroups": [
+    { "query": "path:wiki/entities",    "color": { "a": 1, "rgb": 12945088 } },
+    { "query": "path:wiki/concepts",    "color": { "a": 1, "rgb": 5227007  } },
+    { "query": "path:wiki/sources",     "color": { "a": 1, "rgb": 6986069  } },
+    { "query": "path:wiki/meta",        "color": { "a": 1, "rgb": 5676246  } },
+    { "query": "path:wiki",             "color": { "a": 1, "rgb": 5676246  } }
+  ],
+  "showArrow": true,
+  "textFadeMultiplier": -1,
+  "nodeSizeMultiplier": 1.8,
+  "lineSizeMultiplier": 1.2,
+  "centerStrength": 0.5,
+  "repelStrength": 30,
+  "linkStrength": 1.5,
+  "linkDistance": 120,
+  "scale": 1.0
+}
+EOF
+
+# ── 3. Write app.json (excluded files) ───────────────────────────────────────
+cat > "$OBSIDIAN/app.json" << 'EOF'
+{
+  "userIgnoreFilters": [
+    "agents/",
+    "commands/",
+    "hooks/",
+    "skills/",
+    "_templates/",
+    "README.md",
+    "CLAUDE.md",
+    "WIKI.md",
+    "Welcome.md"
+  ]
+}
+EOF
+
+# ── 4. Write appearance.json (enable CSS snippet) ────────────────────────────
+cat > "$OBSIDIAN/appearance.json" << 'EOF'
+{
+  "enabledCssSnippets": ["vault-colors"]
+}
+EOF
+
+echo ""
+echo "Setup complete."
+echo ""
+echo "Next steps:"
+echo "  1. Open Obsidian"
+echo "  2. Manage Vaults → Open folder as vault → select: $VAULT"
+echo "  3. Install community plugins: Dataview, Templater, Obsidian Git"
+echo "  4. Type /wiki in Claude Code to scaffold your knowledge base"
+echo ""
+echo "Graph view will show only wiki pages, color-coded by type."
+echo "If colors reset after closing Obsidian: open Graph settings → Color groups"
+echo "and re-add them once. After that, they persist permanently."