Remove legacy logs/ directory, consolidate all data under .g3/

This change removes the legacy logs/ directory and consolidates all
session data, error logs, and discovery files under the .g3/ directory.

New directory structure:
- .g3/sessions/<session_id>/session.json - session logs
- .g3/errors/ - error logs (was logs/errors/)
- .g3/background_processes/ - background process logs
- .g3/discovery/ - planner discovery files (was workspace/logs/)

Changes:
- paths.rs: Remove get_logs_dir()/logs_dir(), add get_errors_dir(),
  get_background_processes_dir(), get_discovery_dir()
- session.rs: Anonymous sessions now use .g3/sessions/anonymous_<ts>/
- error_handling.rs: Errors now saved to .g3/errors/
- project.rs: Remove logs_dir() and ensure_logs_dir() methods
- feedback_extraction.rs: Remove logs_dir field and fallback logic
- planner: Use .g3/ for workspace data and .g3/discovery/ for reports
- flock.rs: Look for session metrics in .g3/sessions/
- coach_feedback.rs: Remove fallback to logs/ path
- Update all tests to use new paths
- Update README.md and .gitignore

crates/g3-core/src/error_handling.rs

@@ -129,8 +129,7 @@ impl ErrorContext {
             return;
         }
 
-        let base_logs_dir = crate::logs_dir();
-        let logs_dir = base_logs_dir.join("errors");
+        let logs_dir = crate::paths::get_errors_dir();
         if !logs_dir.exists() {
             if let Err(e) = std::fs::create_dir_all(&logs_dir) {
                 error!("Failed to create error logs directory: {}", e);

crates/g3-core/src/feedback_extraction.rs

@@ -8,10 +8,9 @@
 //!
 //! Used by both autonomous mode (g3-cli) and planning mode (g3-planner).
 
-use crate::{logs_dir, Agent, TaskResult};
+use crate::{Agent, TaskResult};
 use crate::ui_writer::UiWriter;
 use serde_json::Value;
-use std::path::PathBuf;
 use tracing::{debug, warn};
 
 /// Result of feedback extraction with source information
@@ -60,8 +59,6 @@ impl ExtractedFeedback {
 pub struct FeedbackExtractionConfig {
     /// Whether to print debug information
     pub verbose: bool,
-    /// Custom logs directory (overrides default)
-    pub logs_dir: Option<PathBuf>,
     /// Default feedback message if extraction fails
     pub default_feedback: String,
 }
@@ -70,7 +67,6 @@ impl Default for FeedbackExtractionConfig {
     fn default() -> Self {
         Self {
             verbose: false,
-            logs_dir: None,
             default_feedback: "The implementation needs review. Please ensure all requirements are met and the code compiles without errors.".to_string(),
         }
     }
@@ -149,17 +145,10 @@ fn try_extract_last_assistant_message(
     session_id: &str,
     config: &FeedbackExtractionConfig,
 ) -> Option<String> {
-    // Try new .g3/sessions/<session_id>/session.json path first
-    let log_file_path = crate::get_session_file(session_id);
+    let _ = config; // config no longer used but kept for API compatibility
     
-    // Fall back to old logs/ path if new path doesn't exist
-    let log_file_path = if log_file_path.exists() {
-        log_file_path
-    } else {
-        let logs_path = config.logs_dir.clone().unwrap_or_else(logs_dir);
-        logs_path.join(format!("g3_session_{}.json", session_id))
-    };
-
+    // Use .g3/sessions/<session_id>/session.json path
+    let log_file_path = crate::get_session_file(session_id);
     if !log_file_path.exists() {
         debug!("Session log file not found: {:?}", log_file_path);
         return None;
@@ -214,17 +203,10 @@ fn try_extract_from_session_log(
     session_id: &str,
     config: &FeedbackExtractionConfig,
 ) -> Option<String> {
-    // Try new .g3/sessions/<session_id>/session.json path first
-    let log_file_path = crate::get_session_file(session_id);
+    let _ = config; // config no longer used but kept for API compatibility
     
-    // Fall back to old logs/ path if new path doesn't exist
-    let log_file_path = if log_file_path.exists() {
-        log_file_path
-    } else {
-        let logs_path = config.logs_dir.clone().unwrap_or_else(logs_dir);
-        logs_path.join(format!("g3_session_{}.json", session_id))
-    };
-
+    // Use .g3/sessions/<session_id>/session.json path
+    let log_file_path = crate::get_session_file(session_id);
     if !log_file_path.exists() {
         debug!("Session log file not found: {:?}", log_file_path);
         return None;
@@ -358,17 +340,10 @@ fn try_extract_from_conversation_history(
     session_id: &str,
     config: &FeedbackExtractionConfig,
 ) -> Option<String> {
-    // Try new .g3/sessions/<session_id>/session.json path first
-    let log_file_path = crate::get_session_file(session_id);
+    let _ = config; // config no longer used but kept for API compatibility
     
-    // Fall back to old logs/ path if new path doesn't exist
-    let log_file_path = if log_file_path.exists() {
-        log_file_path
-    } else {
-        let logs_path = config.logs_dir.clone().unwrap_or_else(logs_dir);
-        logs_path.join(format!("g3_session_{}.json", session_id))
-    };
-
+    // Use .g3/sessions/<session_id>/session.json path
+    let log_file_path = crate::get_session_file(session_id);
     if !log_file_path.exists() {
         return None;
     }
@@ -652,7 +627,6 @@ mod tests {
     fn test_feedback_extraction_config_default() {
         let config = FeedbackExtractionConfig::default();
         assert!(!config.verbose);
-        assert!(config.logs_dir.is_none());
         assert!(config.default_feedback.contains("review"));
     }
 }

crates/g3-core/src/lib.rs

@@ -53,10 +53,11 @@ use std::time::{Duration, Instant};
 use tokio_util::sync::CancellationToken;
 use tracing::{debug, error, warn};
 
-// Re-export path utilities for backward compatibility
+// Re-export path utilities
 pub use paths::{
-    G3_WORKSPACE_PATH_ENV, ensure_session_dir, get_context_summary_file, get_g3_dir, get_logs_dir,
-    get_session_file, get_session_logs_dir, get_session_todo_path, get_thinned_dir, logs_dir,
+    G3_WORKSPACE_PATH_ENV, ensure_session_dir, get_context_summary_file, get_g3_dir,
+    get_session_file, get_session_logs_dir, get_session_todo_path, get_thinned_dir,
+    get_errors_dir, get_background_processes_dir, get_discovery_dir,
 };
 use paths::get_todo_path;
 
@@ -291,7 +292,7 @@ impl<W: UiWriter> Agent<W> {
             working_dir: None,
             background_process_manager: std::sync::Arc::new(
                 background_process::BackgroundProcessManager::new(
-                    paths::get_logs_dir().join("background_processes")
+                    paths::get_background_processes_dir()
                 )),
             pending_images: Vec::new(),
             is_agent_mode: false,

crates/g3-core/src/paths.rs

@@ -1,8 +1,8 @@
 //! Path utilities for G3 session and workspace management.
 //!
 //! This module centralizes all path-related logic for:
-//! - TODO file location
-//! - Logs directory
+//! - TODO file location  
+//! - Error logs directory
 //! - Session directories and files
 //! - Thinned content storage
 
@@ -33,22 +33,29 @@ pub fn get_session_todo_path(session_id: &str) -> PathBuf {
     get_session_logs_dir(session_id).join("todo.g3.md")
 }
 
-/// Get the path to the logs directory.
+/// Get the path to the errors directory.
 ///
-/// Checks for G3_WORKSPACE_PATH environment variable first (used by planning mode),
-/// then falls back to "logs" in the current directory.
-pub fn get_logs_dir() -> PathBuf {
-    if let Ok(workspace_path) = std::env::var(G3_WORKSPACE_PATH_ENV) {
-        PathBuf::from(workspace_path).join("logs")
-    } else {
-        std::env::current_dir().unwrap_or_default().join("logs")
-    }
+/// Returns `.g3/errors/` in the workspace or current directory.
+pub fn get_errors_dir() -> PathBuf {
+    get_g3_dir().join("errors")
 }
 
-/// Public accessor for the logs directory path (for use by submodules).
-/// Alias for `get_logs_dir()` for backward compatibility.
-pub fn logs_dir() -> PathBuf {
-    get_logs_dir()
+/// Get the path to the background processes directory.
+///
+/// Returns `.g3/background_processes/` in the workspace or current directory.
+pub fn get_background_processes_dir() -> PathBuf {
+    get_g3_dir().join("background_processes")
+}
+
+/// Get the path to the discovery logs directory (for planner mode).
+///
+/// Returns `.g3/discovery/` in the workspace or current directory.
+pub fn get_discovery_dir() -> PathBuf {
+    if let Ok(workspace_path) = std::env::var(G3_WORKSPACE_PATH_ENV) {
+        PathBuf::from(workspace_path).join(".g3").join("discovery")
+    } else {
+        get_g3_dir().join("discovery")
+    }
 }
 
 /// Get the base .g3 directory path.

crates/g3-core/src/project.rs

@@ -127,18 +127,4 @@ impl Project {
         std::env::set_current_dir(&self.workspace_dir)?;
         Ok(())
     }
-
-    /// Get the logs directory for the project
-    pub fn logs_dir(&self) -> PathBuf {
-        self.workspace_dir.join("logs")
-    }
-
-    /// Ensure the logs directory exists
-    pub fn ensure_logs_dir(&self) -> Result<()> {
-        let logs_dir = self.logs_dir();
-        if !logs_dir.exists() {
-            std::fs::create_dir_all(&logs_dir)?;
-        }
-        Ok(())
-    }
 }

crates/g3-core/src/session.rs

@@ -5,7 +5,7 @@
 //! operations from the Agent, keeping the Agent as a thin orchestrator.
 
 use crate::context_window::ContextWindow;
-use crate::paths::{ensure_session_dir, get_context_summary_file, get_g3_dir, get_logs_dir, get_session_file};
+use crate::paths::{ensure_session_dir, get_context_summary_file, get_g3_dir, get_session_file};
 use g3_providers::MessageRole;
 use std::collections::hash_map::DefaultHasher;
 use std::hash::{Hash, Hasher};
@@ -90,7 +90,7 @@ pub fn generate_session_id(description: &str, agent_name: Option<&str>) -> Strin
 /// Save the context window to a session file.
 ///
 /// If session_id is provided, saves to `.g3/sessions/<session_id>/session.json`.
-/// Otherwise, falls back to `logs/g3_context_<timestamp>.json`.
+/// Otherwise, saves to `.g3/sessions/anonymous_<timestamp>/session.json`.
 pub fn save_context_window(
     session_id: Option<&str>,
     context_window: &ContextWindow,
@@ -110,13 +110,13 @@ pub fn save_context_window(
         }
         get_session_file(id)
     } else {
-        // Fallback to old logs/ directory for sessions without ID
-        let logs_dir = get_logs_dir();
-        if let Err(e) = std::fs::create_dir_all(&logs_dir) {
-            error!("Failed to create logs directory: {}", e);
+        // Create anonymous session for sessions without ID
+        let anonymous_id = format!("anonymous_{}", timestamp);
+        if let Err(e) = ensure_session_dir(&anonymous_id) {
+            error!("Failed to create anonymous session directory: {}", e);
             return;
         }
-        logs_dir.join(format!("g3_context_{}.json", timestamp))
+        get_session_file(&anonymous_id)
     };
 
     let context_data = serde_json::json!({
@@ -252,8 +252,8 @@ pub fn log_error_to_session(
         .unwrap_or_default()
         .as_secs();
 
-    let logs_dir = get_logs_dir();
-    let filename = logs_dir.join(format!("g3_session_{}.json", session_id));
+    // Use the new .g3/sessions/<session_id>/session.json path
+    let filename = get_session_file(session_id);
 
     // Read existing session log
     let mut session_data: serde_json::Value = if filename.exists() {

crates/g3-core/tests/background_process_demo_test.rs

@@ -29,7 +29,7 @@ echo "Done!"
         fs::set_permissions(&script_path, fs::Permissions::from_mode(0o755)).unwrap();
     }
     
-    let log_dir = test_dir.join("logs");
+    let log_dir = test_dir.join(".g3").join("background_processes");
     let manager = BackgroundProcessManager::new(log_dir);
     
     println!("\n=== Background Process Demo ===");

crates/g3-core/tests/integration_blackbox_test.rs

@@ -53,7 +53,7 @@ done
             fs::set_permissions(&script_path, fs::Permissions::from_mode(0o755)).unwrap();
         }
 
-        let log_dir = test_dir.join("logs");
+        let log_dir = test_dir.join(".g3").join("background_processes");
         let manager = BackgroundProcessManager::new(log_dir);
 
         // Start the process
@@ -116,7 +116,7 @@ sleep 30
             fs::set_permissions(&script_path, fs::Permissions::from_mode(0o755)).unwrap();
         }
 
-        let log_dir = test_dir.join("logs");
+        let log_dir = test_dir.join(".g3").join("background_processes");
         let manager = BackgroundProcessManager::new(log_dir);
 
         // Start a process
@@ -151,7 +151,7 @@ sleep 30
         let _ = fs::remove_dir_all(&test_dir);
         fs::create_dir_all(&test_dir).unwrap();
 
-        let log_dir = test_dir.join("logs");
+        let log_dir = test_dir.join(".g3").join("background_processes");
         let manager = BackgroundProcessManager::new(log_dir);
 
         // Getting a process that doesn't exist should return None

crates/g3-core/tests/test_session_continuation.rs

@@ -91,7 +91,7 @@ fn test_save_and_load_continuation() {
         "save_load_test".to_string(),
         None,
         Some("Test summary content".to_string()),
-        "/logs/g3_session_save_load_test.json".to_string(),
+        "/.g3/sessions/save_load_test/session.json".to_string(),
         35.5,
         Some("- [ ] Pending task".to_string()),
         temp_dir.path().to_string_lossy().to_string(),
@@ -321,9 +321,9 @@ fn test_has_valid_continuation_with_existing_session_log() {
     let (temp_dir, original_dir) = setup_test_env();
 
     // Create a fake session log file
-    let logs_dir = temp_dir.path().join("logs");
-    fs::create_dir_all(&logs_dir).expect("Failed to create logs dir");
-    let session_log_path = logs_dir.join("g3_session_valid_test.json");
+    let session_dir = temp_dir.path().join(".g3").join("sessions").join("valid_test");
+    fs::create_dir_all(&session_dir).expect("Failed to create session dir");
+    let session_log_path = session_dir.join("session.json");
     fs::write(&session_log_path, "{}").expect("Failed to write session log");
 
     // Create a continuation pointing to the existing session log