fix: Docker stdio communication for Claude Desktop compatibility

Fixed the initialization timeout issue with minimal changes:

1. Added stdout flush after server connection to combat Docker buffering
2. Fixed docker-entrypoint.sh to not output to stdout in stdio mode
3. Added process.stdin.resume() to keep server alive
4. Added IS_DOCKER environment variable for future use
5. Updated README to prioritize Docker with correct -i flag configuration

The core issue was Docker's block buffering preventing immediate JSON-RPC
responses. The -i flag maintains stdin connection, and explicit flushing
ensures responses reach Claude Desktop immediately.

Also fixed "Shutting down..." message that was breaking JSON-RPC protocol
by redirecting it to stderr in stdio mode.

Docker is now the recommended installation method as originally intended.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

docker/docker-entrypoint.sh

@@ -33,7 +33,12 @@ if [ "$(id -u)" = "0" ]; then
 fi
 
 # Trap signals for graceful shutdown
-trap 'echo "Shutting down..."; kill -TERM $PID' TERM INT
+# In stdio mode, don't output anything to stdout as it breaks JSON-RPC
+if [ "$MCP_MODE" = "stdio" ]; then
+    trap 'kill -TERM $PID 2>/dev/null' TERM INT
+else
+    trap 'echo "Shutting down..." >&2; kill -TERM $PID' TERM INT
+fi
 
 # Execute the main command in background
 "$@" &