reorganize files and logic into cleaner structure

Author: alexylon

.sofosrc

@@ -14,18 +14,18 @@ Sofos is a terminal-based AI coding assistant powered by Anthropic's Claude API.
 
 ### Key Design Decisions
 
-1. **Dual Session Storage Format** (src/history.rs)
+1. **Dual Session Storage Format** (src/session/history.rs)
    - `api_messages`: Anthropic API format for continuing conversations
    - `display_messages`: UI-friendly format for showing conversation history
    - This separation ensures Claude sees proper API format while users see original UI
 
-2. **Tool Calling Pattern** (src/repl.rs)
+2. **Tool Calling Pattern** (src/repl/mod.rs)
    - Assistant returns content blocks (text + tool_use)
    - REPL executes tools and collects results
    - Results sent back as user message with tool_result blocks
    - **Loop-based handling** allows Claude to use multiple tools in sequence iteratively
 
-3. **Two-Level Instructions** (src/history.rs)
+3. **Two-Level Instructions** (src/session/history.rs)
    - `.sofosrc`: Project-level, version controlled
    - `.sofos/instructions.md`: Personal, gitignored
    - Both appended to system prompt at startup
@@ -43,27 +43,47 @@ Sofos is a terminal-based AI coding assistant powered by Anthropic's Claude API.
 
 ```
 src/
-├── api/                    # Anthropic API integration
-│   ├── client.rs          # HTTP client for Claude API
-│   ├── morph.rs           # Morph Apply API client (optional)
-│   ├── types.rs           # Message types and serialization
-│   └── mod.rs
-├── tools/                  # Tool implementations
-│   ├── filesystem.rs      # File operations (read, write, list, etc)
-│   ├── bashexec.rs        # Sandboxed bash execution
-│   ├── codesearch.rs      # Ripgrep integration
-│   ├── permissions.rs     # 3-tier command permission system
-│   ├── types.rs           # Tool definitions for API
-│   └── mod.rs
-├── conversation.rs         # Message history management
-├── diff.rs                 # Contextual diff generation and display
-├── history.rs              # Session persistence + custom instructions
-├── repl.rs                 # Main REPL loop and display logic
-├── syntax.rs               # Markdown/code syntax highlighting
-├── cli.rs                  # Command-line argument parsing
-├── error.rs                # Error types
-├── session_selector.rs     # TUI for session selection
-└── main.rs                 # Entry point
+├── main.rs              # Entry point
+├── cli.rs               # CLI argument parsing
+├── error.rs             # Error types
+├── error_ext.rs         # Error extensions
+├── config.rs            # Configuration (SofosConfig, ModelConfig)
+│
+├── api/                 # API clients
+│   ├── anthropic.rs     # Claude API client
+│   ├── openai.rs        # OpenAI API client
+│   ├── morph.rs         # Morph Apply API client
+│   ├── types.rs         # Message types and serialization
+│   └── utils.rs         # API utilities
+│
+├── repl/                # REPL components
+│   ├── mod.rs           # Main REPL loop and Repl struct
+│   ├── conversation.rs  # Message history management
+│   ├── prompt.rs        # Prompt rendering
+│   ├── request_builder.rs   # API request construction
+│   └── response_handler.rs  # Response processing
+│
+├── session/             # Session management
+│   ├── history.rs       # Session persistence + custom instructions
+│   ├── state.rs         # Runtime session state
+│   └── selector.rs      # Session selection TUI
+│
+├── tools/               # Tool implementations
+│   ├── filesystem.rs    # File operations (read, write, list, etc)
+│   ├── bashexec.rs      # Sandboxed bash execution
+│   ├── codesearch.rs    # Ripgrep integration
+│   ├── image.rs         # Image handling
+│   ├── permissions.rs   # 3-tier command permission system
+│   ├── types.rs         # Tool definitions for API
+│   └── utils.rs         # Tool utilities
+│
+├── ui/                  # UI components
+│   ├── mod.rs           # Main UI utilities and display logic
+│   ├── syntax.rs        # Markdown/code syntax highlighting
+│   └── diff.rs          # Contextual diff generation and display
+│
+└── commands/            # Built-in commands
+    └── builtin.rs       # Command implementations
 ```
 
 ### Key Files
@@ -73,25 +93,28 @@ src/
 - Handles serialization/deserialization for Anthropic API
 - Supports both regular and server-side tools (like web_search)
 
-**src/diff.rs**
+**src/ui/diff.rs**
 - Generate contextual diffs showing only changed code blocks
 - Uses `similar` crate for accurate line-by-line diffing
 - Formats output with colored backgrounds (red for deletions, blue for additions)
 - Context lines (default: 2) show unchanged code around changes
 - Used by morph_edit_file tool to display what changed
 
-**src/history.rs**
+**src/session/history.rs**
 - SessionMetadata: Preview and timestamps for session list
 - Session: Dual storage (api_messages + display_messages)
 - DisplayMessage: Enum for user messages, assistant responses, and tool executions
 
-**src/repl.rs**
+**src/repl/mod.rs**
 - Main event loop (run method)
-- handle_response: Recursively processes assistant responses and tool calls
-- display_session: Reconstructs conversation UI when resuming
-- Max recursion depth: 50 (prevents infinite loops)
+- Manages REPL state and user interaction
+- Coordinates conversation, tools, and UI
 
-**src/conversation.rs**
+**src/repl/response_handler.rs**
+- Iteratively processes assistant responses and tool calls
+- Max iterations: 200 (prevents infinite loops)
+
+**src/repl/conversation.rs**
 - Manages in-memory message history
 - Trims to MAX_MESSAGES (500) to prevent token overflow
 - Builds system prompt with features list and custom instructions
@@ -222,7 +245,7 @@ src/
 
 **Problem:** Claude can make infinite tool calls if it gets stuck in a loop
 
-**Solution:** (repl.rs:handle_response)
+**Solution:** (src/repl/response_handler.rs)
 - Use an **iterative loop** instead of recursion for constant stack space
 - Track iteration count in the loop
 - MAX_TOOL_ITERATIONS = 200

README.md

@@ -246,7 +246,52 @@ cargo build --release         # Build release
 RUST_LOG=debug sofos          # Debug logging
 ```
 
-**Structure:** `src/` (api, tools, commands, repl, ui, conversation, history, config, etc.), `tests/`, `assets/`, `.sofos/` (gitignored), `.sofosrc` (version controlled)
+**Structure:**
+
+```
+src/
+├── main.rs              # Entry point
+├── cli.rs               # CLI argument parsing
+├── error.rs             # Error types
+├── error_ext.rs         # Error extensions
+├── config.rs            # Configuration (SofosConfig, ModelConfig)
+│
+├── api/                 # API clients
+│   ├── anthropic.rs     # Claude API client
+│   ├── openai.rs        # OpenAI API client
+│   ├── morph.rs         # Morph Apply API client
+│   ├── types.rs         # Message types and serialization
+│   └── utils.rs         # API utilities
+│
+├── repl/                # REPL components
+│   ├── mod.rs           # Main REPL loop
+│   ├── conversation.rs  # Message history management
+│   ├── prompt.rs        # Prompt rendering
+│   ├── request_builder.rs   # API request construction
+│   └── response_handler.rs  # Response processing
+│
+├── session/             # Session management
+│   ├── history.rs       # Session persistence
+│   ├── state.rs         # Runtime session state
+│   └── selector.rs      # Session selection TUI
+│
+├── tools/               # Tool implementations
+│   ├── filesystem.rs    # File operations
+│   ├── bashexec.rs      # Bash execution
+│   ├── codesearch.rs    # Code search (ripgrep)
+│   ├── image.rs         # Image handling
+│   ├── permissions.rs   # Permission system
+│   ├── types.rs         # Tool definitions
+│   └── utils.rs         # Tool utilities
+│
+├── ui/                  # UI components
+│   ├── mod.rs           # Main UI utilities
+│   ├── syntax.rs        # Syntax highlighting
+│   └── diff.rs          # Diff generation
+│
+└── commands/            # Built-in commands
+    └── builtin.rs       # Command implementations
+```
 
 See `.sofosrc` for detailed conventions.
 

src/config.rs

@@ -1,17 +1,11 @@
 /// Central configuration for Sofos
 #[derive(Debug, Clone)]
 pub struct SofosConfig {
-    /// Maximum number of messages to keep in conversation history
     pub max_messages: usize,
-    /// Maximum context tokens to send to API (includes system prompt and messages)
-    /// Set to 180,000 to leave buffer below API's 200,000 limit
     pub max_context_tokens: usize,
-    /// Maximum number of tool execution iterations to prevent infinite loops
     pub max_tool_iterations: u32,
-    /// Maximum file size for read operations (in bytes)
     #[allow(dead_code)]
     pub max_file_size: usize,
-    /// Maximum bash command output size (in bytes)
     #[allow(dead_code)]
     pub max_bash_output: usize,
 }
@@ -22,12 +16,41 @@ impl Default for SofosConfig {
             max_messages: 500,
             max_context_tokens: 180_000,
             max_tool_iterations: 200,
-            max_file_size: 10 * 1024 * 1024,   // 10MB
-            max_bash_output: 50 * 1024 * 1024, // 50MB
+            max_file_size: 10 * 1024 * 1024,
+            max_bash_output: 50 * 1024 * 1024,
         }
     }
 }
 
+/// Configuration for the language model
+#[derive(Clone)]
+pub struct ModelConfig {
+    pub model: String,
+    pub max_tokens: u32,
+    pub enable_thinking: bool,
+    pub thinking_budget: u32,
+}
+
+impl ModelConfig {
+    pub fn new(
+        model: String,
+        max_tokens: u32,
+        enable_thinking: bool,
+        thinking_budget: u32,
+    ) -> Self {
+        Self {
+            model,
+            max_tokens,
+            enable_thinking,
+            thinking_budget,
+        }
+    }
+
+    pub fn set_thinking(&mut self, enabled: bool) {
+        self.enable_thinking = enabled;
+    }
+}
+
 impl SofosConfig {
     // No need for new() since Default::default() is the idiomatic way
 }

src/main.rs

@@ -2,19 +2,10 @@ mod api;
 mod cli;
 mod commands;
 mod config;
-mod conversation;
-mod diff;
 mod error;
 mod error_ext;
-mod history;
-mod model_config;
-mod prompt;
 mod repl;
-mod request_builder;
-mod response_handler;
-mod session_selector;
-mod session_state;
-mod syntax;
+mod session;
 mod tools;
 mod ui;
 
@@ -23,8 +14,8 @@ use clap::Parser;
 use cli::Cli;
 use colored::Colorize;
 use error::Result;
-use history::HistoryManager;
 use repl::{Repl, ReplConfig};
+use session::HistoryManager;
 use std::env;
 use ui::UI;
 
@@ -115,7 +106,7 @@ fn main() -> Result<()> {
         let history_manager = HistoryManager::new(workspace)?;
         let sessions = history_manager.list_sessions()?;
 
-        if let Some(session_id) = session_selector::select_session(sessions)? {
+        if let Some(session_id) = session::select_session(sessions)? {
             repl.load_session_by_id(&session_id)?;
             println!();
         }

src/model_config.rs

@@ -1,15 +1,19 @@
+pub mod conversation;
+mod prompt;
+mod request_builder;
+mod response_handler;
+
+pub use conversation::ConversationHistory;
+pub use prompt::ReplPrompt;
+pub use request_builder::RequestBuilder;
+pub use response_handler::ResponseHandler;
+
 use crate::api::LlmClient::Anthropic;
 use crate::api::{CreateMessageRequest, ImageSource, LlmClient, MessageContentBlock, MorphClient};
 use crate::commands::{Command, CommandResult};
-use crate::config::{NORMAL_MODE_MESSAGE, SAFE_MODE_MESSAGE};
-use crate::conversation::ConversationHistory;
+use crate::config::{ModelConfig, NORMAL_MODE_MESSAGE, SAFE_MODE_MESSAGE};
 use crate::error::{Result, SofosError};
-use crate::history::{DisplayMessage, HistoryManager};
-use crate::model_config::ModelConfig;
-use crate::prompt::ReplPrompt;
-use crate::request_builder::RequestBuilder;
-use crate::response_handler::ResponseHandler;
-use crate::session_state::SessionState;
+use crate::session::{DisplayMessage, HistoryManager, SessionState};
 use crate::tools::image::{extract_image_references, ImageLoader, ImageReference};
 use crate::tools::ToolExecutor;
 use crate::ui::{set_safe_mode_cursor_style, UI};
@@ -483,7 +487,7 @@ impl Repl {
             return Ok(());
         }
 
-        let selected_id = crate::session_selector::select_session(sessions)?;
+        let selected_id = crate::session::select_session(sessions)?;
 
         if let Some(session_id) = selected_id {
             self.load_session_by_id(&session_id)?;

src/conversation.rs src/repl/conversation.rssrc/conversation.rs renamed to src/repl/conversation.rs

@@ -1,6 +1,6 @@
 use crate::api::LlmClient::{Anthropic, OpenAI};
 use crate::api::{CreateMessageRequest, LlmClient, Tool};
-use crate::conversation::ConversationHistory;
+use crate::repl::conversation::ConversationHistory;
 
 pub struct RequestBuilder<'a> {
     client: &'a LlmClient,

src/repl.rs src/repl/mod.rssrc/repl.rs renamed to src/repl/mod.rs

@@ -1,9 +1,9 @@
 use crate::api::{ContentBlock, CreateMessageRequest, LlmClient};
 use crate::config::SofosConfig;
-use crate::conversation::ConversationHistory;
 use crate::error::{Result, SofosError};
-use crate::history::DisplayMessage;
-use crate::request_builder::RequestBuilder;
+use crate::repl::conversation::ConversationHistory;
+use crate::repl::request_builder::RequestBuilder;
+use crate::session::DisplayMessage;
 use crate::tools::ToolExecutor;
 use crate::ui::UI;
 use colored::Colorize;