feat: integrate daemon mode with MCP server via --watch flag

Add automatic file watching to MCP server startup:
- DaemonConfig in codegraph-core for daemon settings
- DaemonManager wrapper coordinates daemon lifecycle with MCP server
- CLI flags: --watch, --watch-path, --no-watch for stdio/http transports
- Non-blocking startup: daemon runs in background tokio task
- Error isolation: daemon failures don't crash MCP server
- Graceful cleanup: daemon stops when MCP server exits
- Config support: [daemon].auto_start_with_mcp enables by default
- Environment variables: CODEGRAPH_DAEMON_AUTO_START, CODEGRAPH_DAEMON_WATCH_PATH

Usage: codegraph start stdio --watch

Author: jruokola

CHANGELOG.md

@@ -22,6 +22,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - **Event coalescing**: Batches rapid file changes to avoid redundant re-indexing
 - **Feature flag**: `daemon` feature enables this functionality
 
+#### **MCP Server Integration with Daemon (`--watch`)**
+- **Integrated daemon with MCP server**: `codegraph start stdio --watch` starts the daemon automatically
+- **Non-blocking startup**: Daemon runs in background task, MCP server starts immediately
+- **Error isolation**: Daemon failures don't crash MCP server
+- **CLI flags for MCP server**:
+  - `--watch` - Enable automatic file watching (also via `CODEGRAPH_DAEMON_AUTO_START` env var)
+  - `--watch-path <PATH>` - Specify directory to watch (also via `CODEGRAPH_DAEMON_WATCH_PATH` env var)
+  - `--no-watch` - Explicitly disable daemon even if config enables it
+- **Configuration support**: `[daemon].auto_start_with_mcp` in config.toml to enable by default
+- **DaemonConfig**: New configuration struct in `codegraph-core` for daemon settings
+- **DaemonManager**: Coordinates daemon lifecycle with MCP server lifecycle
+- **Graceful cleanup**: Daemon stops automatically when MCP server exits
+
 ### Removed
 - Dropped the transactional/versioning/branch N-API bindings plus their documentation; the native TypeScript surface now focuses on semantic search, graph analysis, and cloud configuration so it matches the Surreal-only architecture.
 - Replaced the native addon example with a semantic-search walkthrough and removed CLI-centric integration snippets that referenced the deleted CodeGraph CLI.

README.md

@@ -581,7 +581,34 @@ codegraph daemon stop /path/to/project
 
 **Note:** Requires the `daemon` feature flag:
 ```bash
-cargo build --release -p codegraph-mcp --features "daemon,ai-enhanced,ollama"
+cargo build --release -p codegraph-mcp --features "daemon,ai-enhanced"
+```
+
+### MCP Server with Auto-Watching (`--watch`)
+
+Start the MCP server with automatic file watching - the daemon runs in the background:
+
+```bash
+# Start MCP server with file watching
+codegraph start stdio --watch
+
+# Watch a specific directory
+codegraph start stdio --watch --watch-path /path/to/project
+
+# Disable watching even if enabled in config
+codegraph start stdio --no-watch
+
+# Via environment variable
+CODEGRAPH_DAEMON_AUTO_START=true codegraph start stdio
+```
+
+**Configuration in `~/.codegraph/config.toml`:**
+```toml
+[daemon]
+auto_start_with_mcp = true  # Auto-start daemon when MCP server starts
+debounce_ms = 30
+batch_timeout_ms = 200
+exclude_patterns = ["**/node_modules/**", "**/target/**"]
 ```
 
 **Note:** HTTP transport is not yet implemented with the official rmcp SDK. Use STDIO transport for all MCP integrations.

crates/codegraph-core/src/config_manager.rs

@@ -39,6 +39,10 @@ pub struct CodeGraphConfig {
     /// Logging configuration
     #[serde(default)]
     pub logging: LoggingConfig,
+
+    /// Daemon configuration for automatic file watching
+    #[serde(default)]
+    pub daemon: DaemonConfig,
 }
 
 /// Embedding provider configuration
@@ -287,6 +291,57 @@ impl Default for LoggingConfig {
     }
 }
 
+/// Daemon configuration for automatic file watching and re-indexing
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct DaemonConfig {
+    /// Enable automatic daemon startup with MCP server
+    #[serde(default)]
+    pub auto_start_with_mcp: bool,
+
+    /// Project path to watch (defaults to current directory)
+    #[serde(default)]
+    pub project_path: Option<PathBuf>,
+
+    /// Debounce duration for file changes (ms)
+    #[serde(default = "default_daemon_debounce_ms")]
+    pub debounce_ms: u64,
+
+    /// Batch timeout for collecting changes (ms)
+    #[serde(default = "default_daemon_batch_timeout_ms")]
+    pub batch_timeout_ms: u64,
+
+    /// Health check interval (seconds)
+    #[serde(default = "default_daemon_health_check_interval")]
+    pub health_check_interval_secs: u64,
+
+    /// Languages to watch (empty = all detected)
+    #[serde(default)]
+    pub languages: Vec<String>,
+
+    /// Exclude patterns (gitignore format)
+    #[serde(default = "default_daemon_exclude_patterns")]
+    pub exclude_patterns: Vec<String>,
+
+    /// Include patterns (gitignore format)
+    #[serde(default)]
+    pub include_patterns: Vec<String>,
+}
+
+impl Default for DaemonConfig {
+    fn default() -> Self {
+        Self {
+            auto_start_with_mcp: false, // Opt-in by default
+            project_path: None,
+            debounce_ms: default_daemon_debounce_ms(),
+            batch_timeout_ms: default_daemon_batch_timeout_ms(),
+            health_check_interval_secs: default_daemon_health_check_interval(),
+            languages: vec![],
+            exclude_patterns: default_daemon_exclude_patterns(),
+            include_patterns: vec![],
+        }
+    }
+}
+
 // Default value functions
 fn default_embedding_provider() -> String {
     "auto".to_string()
@@ -353,6 +408,28 @@ fn default_log_format() -> String {
     "pretty".to_string()
 }
 
+// Daemon default functions
+fn default_daemon_debounce_ms() -> u64 {
+    30
+}
+fn default_daemon_batch_timeout_ms() -> u64 {
+    200
+}
+fn default_daemon_health_check_interval() -> u64 {
+    30
+}
+fn default_daemon_exclude_patterns() -> Vec<String> {
+    vec![
+        "**/node_modules/**".to_string(),
+        "**/target/**".to_string(),
+        "**/.git/**".to_string(),
+        "**/build/**".to_string(),
+        "**/.codegraph/**".to_string(),
+        "**/dist/**".to_string(),
+        "**/__pycache__/**".to_string(),
+    ]
+}
+
 /// Configuration manager with smart defaults and auto-detection
 pub struct ConfigManager {
     config: CodeGraphConfig,
@@ -553,6 +630,25 @@ impl ConfigManager {
             config.logging.level = level;
         }
 
+        // Daemon configuration
+        if let Ok(auto_start) = std::env::var("CODEGRAPH_DAEMON_AUTO_START") {
+            config.daemon.auto_start_with_mcp =
+                auto_start.to_lowercase() == "true" || auto_start == "1";
+        }
+        if let Ok(path) = std::env::var("CODEGRAPH_DAEMON_WATCH_PATH") {
+            config.daemon.project_path = Some(PathBuf::from(path));
+        }
+        if let Ok(debounce) = std::env::var("CODEGRAPH_DAEMON_DEBOUNCE_MS") {
+            if let Ok(ms) = debounce.parse() {
+                config.daemon.debounce_ms = ms;
+            }
+        }
+        if let Ok(batch) = std::env::var("CODEGRAPH_DAEMON_BATCH_TIMEOUT_MS") {
+            if let Ok(ms) = batch.parse() {
+                config.daemon.batch_timeout_ms = ms;
+            }
+        }
+
         config
     }