Enhance tool documentation and add new features

- Added module-level documentation for memory tools (`remember`, `recall`, `forget`) to clarify their purpose.
- Improved documentation in `recall.rs` and `remember.rs` to describe the functionality and flow of memory entry operations.
- Updated `mod.rs` to include descriptions for the tool trait and execution context.
- Enhanced `plan.rs` with detailed comments on plan-mode signaling tools.
- Documented text search tools in `search.rs` to explain their functionality.
- Improved sequential-thinking tool documentation in `seqthink.rs`.
- Added safety filter documentation in `shell_filter` for credential and git operations.
- Enhanced utility tools documentation, including `cd`, `dir_cache_update`, and `todowrite`.
- Improved rendering documentation in view modules (`chat`, `markdown`, `status`, `workflow`) to clarify rendering flows and purposes.

src/ipc/protocol.rs

@@ -1,5 +1,19 @@
+//! Wire message types exchanged between an attached client and the
+//! daemon over the `Connection`/framing layer (`conn.rs`, `frame.rs`).
+//!
+//! Flow: client input events are captured as `KeyAction`/`ClientRequest`
+//! and sent to the daemon → the daemon applies them to its `AppStateRest`
+//! and replies with `DaemonFrame` variants (a flattened `StatePayload`
+//! for redraw, streamed tokens, system notes, or a close signal).
+//!
+//! Why: `StatePayload`/`MessageEntry`/`ToastEntry` are deliberately flat,
+//! serializable projections of daemon-side state so the client can
+//! redraw its TUI without sharing any in-process state with the daemon.
+
 use serde::{Deserialize, Serialize};
 
+/// Wire-serializable subset of `crossterm::event::KeyCode`, sent from
+/// an attached client to the daemon over IPC.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub enum KeyAction {
     Char(char),
@@ -19,6 +33,8 @@ pub enum KeyAction {
     Function(u8),
 }
 
+/// Messages an attached client sends to the daemon: input events, a
+/// full-line submit, terminal resize, and connection lifecycle.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub enum ClientRequest {
     Tick,
@@ -33,6 +49,7 @@ pub enum ClientRequest {
     Close,
 }
 
+/// Flattened chat message sent from daemon to client for transcript display.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct MessageEntry {
     pub role: String,
@@ -40,6 +57,7 @@ pub struct MessageEntry {
     pub timestamp: i64,
 }
 
+/// Flattened toast notification sent from daemon to client for rendering.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct ToastEntry {
     pub kind: String,
@@ -48,6 +66,8 @@ pub struct ToastEntry {
     pub lifetime_ms: u64,
 }
 
+/// Snapshot of daemon-side `AppStateRest` sent to the client after every
+/// action, enough for the client to redraw its TUI without shared state.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct StatePayload {
     pub session_id: String,
@@ -61,6 +81,7 @@ pub struct StatePayload {
     pub input_cursor: usize,
 }
 
+/// Messages the daemon sends back to an attached client.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub enum DaemonFrame {
     StateUpdate(Box<StatePayload>),