Complete daemon RPC with per-request context routing (bd-115)

- MCP server now uses daemon client by default with CLI fallback
- Added BEADS_USE_DAEMON environment variable (default: enabled)
- Created multi-repo integration test (all tests pass)
- Updated .gitignore for daemon runtime files
- Added SETUP_DAEMON.md with migration instructions
- Closed bd-105 (investigation complete) and bd-114 (multi-server confusion)

This enables single MCP server to handle multiple repos via daemon
with per-request context routing. No more multiple MCP server configs!

Amp-Thread-ID: https://ampcode.com/threads/T-c222692e-f6ef-4649-9726-db59470b82ef
Co-authored-by: Amp <amp@ampcode.com>

integrations/beads-mcp/SETUP_DAEMON.md

@@ -0,0 +1,202 @@
+# Setting Up Daemon-Based MCP Server
+
+## Quick Start
+
+Replace your multiple MCP server configs with a single daemon-based one:
+
+### 1. Claude Desktop Config
+
+Edit `~/Library/Application Support/Claude/claude_desktop_config.json`:
+
+```json
+{
+  "mcpServers": {
+    "beads": {
+      "command": "beads-mcp",
+      "env": {
+        "BEADS_USE_DAEMON": "1"
+      }
+    }
+  }
+}
+```
+
+**Remove old configs** like `beads-wyvern`, `beads-adar`, etc.
+
+### 2. Start the Daemon
+
+In your beads project directory:
+
+```bash
+bd daemon start
+```
+
+The daemon will:
+- Listen on `.beads/bd.sock`
+- Route operations to correct database based on request cwd
+- Handle multiple repos simultaneously
+
+### 3. Test It
+
+```bash
+# Test with beads repo
+cd ~/src/vc/adar/beads
+bd list
+
+# Test with another repo
+cd ~/src/vc/wyvern
+bd list
+
+# Both should show correct issues for their respective databases
+```
+
+### 4. Restart Claude Desktop
+
+After updating the config, restart Claude Desktop to load the new MCP server configuration.
+
+## How It Works
+
+```
+Claude/Amp → Single MCP Server → Daemon Client → Daemon → Correct Database
+                  ↓ 
+          Uses set_context to pass workspace_root
+                  ↓
+          Daemon uses cwd to find .beads/*.db
+```
+
+- **No more multiple MCP servers** - one server handles all repos
+- **Per-request routing** - daemon finds correct database for each operation
+- **Automatic fallback** - if daemon not running, falls back to CLI mode
+- **Concurrent access** - daemon handles multiple repos at once
+
+## Advanced Configuration
+
+### Optional Environment Variables
+
+```json
+{
+  "mcpServers": {
+    "beads": {
+      "command": "beads-mcp",
+      "env": {
+        "BEADS_USE_DAEMON": "1",
+        "BEADS_REQUIRE_CONTEXT": "1",
+        "BEADS_ACTOR": "claude"
+      }
+    }
+  }
+}
+```
+
+- `BEADS_USE_DAEMON` - Use daemon (default: `1`)
+- `BEADS_REQUIRE_CONTEXT` - Enforce set_context before writes (default: `0`)
+- `BEADS_ACTOR` - Actor name for audit trail (default: `$USER`)
+
+### Disable Daemon (Fallback to CLI)
+
+If you want to temporarily use CLI mode:
+
+```json
+{
+  "env": {
+    "BEADS_USE_DAEMON": "0"
+  }
+}
+```
+
+## Daemon Management
+
+```bash
+# Start daemon
+bd daemon start
+
+# Check status
+bd daemon status
+
+# View logs
+bd daemon logs
+
+# Stop daemon
+bd daemon stop
+
+# Restart daemon
+bd daemon stop && bd daemon start
+```
+
+## Troubleshooting
+
+### "Daemon not running" errors
+
+Start the daemon in your beads project:
+```bash
+cd ~/src/vc/adar/beads
+bd daemon start
+```
+
+### Wrong database being used
+
+1. Check where daemon is running:
+   ```bash
+   bd daemon status
+   ```
+
+2. Use `set_context` tool in Claude to set workspace root:
+   ```
+   set_context /path/to/your/project
+   ```
+
+3. Verify with `where_am_i` tool
+
+### Multiple repos not working
+
+Ensure:
+- Daemon is running in a parent directory that can reach all repos
+- Each repo has `.beads/*.db` properly initialized
+- MCP server is passing correct workspace_root via `set_context`
+
+## Migration from Multi-Server Setup
+
+### Old Config (Remove This)
+
+```json
+{
+  "mcpServers": {
+    "beads-adar": {
+      "command": "beads-mcp",
+      "env": {
+        "BEADS_DB": "/path/to/adar/.beads/bd.db"
+      }
+    },
+    "beads-wyvern": {
+      "command": "beads-mcp",
+      "env": {
+        "BEADS_DB": "/path/to/wyvern/.beads/wy.db"
+      }
+    }
+  }
+}
+```
+
+### New Config (Use This)
+
+```json
+{
+  "mcpServers": {
+    "beads": {
+      "command": "beads-mcp",
+      "env": {
+        "BEADS_USE_DAEMON": "1"
+      }
+    }
+  }
+}
+```
+
+## Benefits
+
+✅ Single MCP server for all repos
+✅ No manual BEADS_DB configuration per repo
+✅ Automatic context switching
+✅ Better performance (no process spawning per operation)
+✅ Concurrent multi-repo operations
+✅ Simpler configuration