docs: Document multi-repo workflow with global daemon

Implements bd-122: Document how to use beads across multiple projects

Added comprehensive multi-repo documentation:
- README.md: Global daemon section with architecture diagram
- AGENTS.md: MCP multi-repo configuration (global daemon + per-project)
- integrations/beads-mcp/README.md: BEADS_WORKING_DIR usage
- Mermaid diagram showing one daemon serving multiple repos

Documentation covers:
- Global daemon (bd daemon --global) for system-wide usage
- Per-project MCP instances with BEADS_WORKING_DIR
- Comparison table (local vs global)
- When to use each approach
- Example workflows for multi-project setups

Benefits of global daemon:
- One daemon process for all repos
- Automatic socket discovery (local -> global fallback)
- Better resource usage
- Per-request context routing to correct database

Amp-Thread-ID: https://ampcode.com/threads/T-ea606216-b886-4af0-bba8-56d000362d01
Co-authored-by: Amp <amp@ampcode.com>

AGENTS.md

@@ -40,6 +40,60 @@ pip install beads-mcp
 
 See `integrations/beads-mcp/README.md` for complete documentation.
 
+### Multi-Repo Configuration (MCP Server)
+
+**Working on multiple projects?** You can configure beads MCP to work across multiple repositories.
+
+**Option 1: Global Daemon (Recommended - v0.9.11+)**
+Start a single daemon to serve all your projects:
+```bash
+# Start global daemon
+bd daemon --global
+
+# MCP server automatically discovers and uses the global daemon
+```
+
+Your MCP config stays simple:
+```json
+{
+  "beads": {
+    "command": "beads-mcp",
+    "args": []
+  }
+}
+```
+
+The MCP server will:
+1. Check for local daemon socket (`.beads/bd.sock`)
+2. Fall back to global daemon socket (`~/.beads/bd.sock`)
+3. Automatically route requests to the correct database based on your current working directory
+
+**Option 2: Multiple MCP Server Instances**
+Configure separate MCP servers for each major project:
+```json
+{
+  "beads-webapp": {
+    "command": "beads-mcp",
+    "env": {
+      "BEADS_WORKING_DIR": "/Users/you/projects/webapp"
+    }
+  },
+  "beads-api": {
+    "command": "beads-mcp",
+    "env": {
+      "BEADS_WORKING_DIR": "/Users/you/projects/api"
+    }
+  }
+}
+```
+
+Each MCP instance will use its specified working directory to find the correct `.beads/*.db` database.
+
+**Which approach should you use?**
+- ✅ **Global daemon**: Best for 3+ projects, better resource usage, automatic routing
+- ✅ **Multiple instances**: Best for 1-2 projects you switch between frequently
+- ✅ **Hybrid**: Run global daemon + use MCP instances for convenience
+
 ### CLI Quick Reference
 
 If you're not using the MCP server, here are the CLI commands: