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>

.gitignore

@@ -33,5 +33,10 @@ Thumbs.db
 *.db-wal
 *.db-shm
 
+# Daemon runtime files
+.beads/daemon.log
+.beads/daemon.pid
+.beads/bd.sock
+
 # Keep JSONL exports (source of truth for git)
 !.beads/*.jsonl