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/model/conversation.rs

@@ -1,5 +1,9 @@
+//! In-memory conversation state: message history plus the system prompt and
+//! model parameters used to drive the LLM.
+
 use serde::{Deserialize, Serialize};
 
+/// A single conversation's message history and generation settings.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct Conversation {
     pub messages: Vec<crate::dto::chat::message::ChatMessage>,
@@ -11,6 +15,8 @@ pub struct Conversation {
 }
 
 impl Conversation {
+    /// Create an empty conversation with the given system prompt and
+    /// session id, using default model/token/temperature settings.
     pub fn new(system_prompt: String, session_id: String) -> Self {
         Conversation {
             messages: Vec::new(),
@@ -22,10 +28,17 @@ impl Conversation {
         }
     }
 
+    /// Append a message to the conversation history.
     pub fn push(&mut self, msg: crate::dto::chat::message::ChatMessage) {
         self.messages.push(msg);
     }
 
+    /// Replace the system prompt and strip any prior `System`-role
+    /// messages from history.
+    ///
+    /// Why: the system prompt is re-injected fresh at request time via
+    /// `to_api_messages`, so stale `System` messages in `self.messages`
+    /// would be redundant/conflicting if left in place.
     pub fn rebuild_system(&mut self, new_prompt: String) {
         self.system_prompt = new_prompt;
         self.messages.retain(|m| {
@@ -33,6 +46,11 @@ impl Conversation {
         });
     }
 
+    /// Build the message list to send to the LLM API, with the system
+    /// prompt prepended.
+    ///
+    /// Return: a new `Vec` (clone of history) with a synthesized system
+    /// message at index 0.
     pub fn to_api_messages(&self) -> Vec<crate::dto::chat::message::ChatMessage> {
         let mut msgs = Vec::with_capacity(self.messages.len() + 1);
         msgs.push(crate::dto::chat::message::ChatMessage::system(&self.system_prompt));
@@ -40,6 +58,8 @@ impl Conversation {
         msgs
     }
 
+    /// Number of messages in the conversation history (excluding the
+    /// synthesized system message).
     pub fn len(&self) -> usize {
         self.messages.len()
     }