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/settings.rs

@@ -1,5 +1,15 @@
+//! User-configurable settings persisted as JSON in the store's base directory.
+//!
+//! `Settings::load` / `Settings::save` are the only entry points; every field
+//! falls back to a hardcoded default via `Default for Settings` when the file
+//! is missing or fails to parse.
+
 use serde::{Deserialize, Serialize};
 
+/// Controls how much network access the agent is permitted during a session.
+///
+/// `Off` disables outbound requests entirely, `ReadOnly` allows fetches but
+/// no mutating calls, `Full` permits everything. Defaults to `Off`.
 #[derive(Debug, Clone, PartialEq, Eq, Serialize, Deserialize)]
 #[derive(Default)]
 pub enum InternetMode {
@@ -11,6 +21,10 @@ pub enum InternetMode {
 
 
 
+/// Top-level application settings, serialized to `settings.json` in the store dir.
+///
+/// Why: a single flat struct rather than nested config so the JSON file stays
+/// human-editable; unknown/missing fields on load fall back to `Default`.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct Settings {
     pub internet_mode: InternetMode,
@@ -49,6 +63,12 @@ impl Default for Settings {
 }
 
 impl Settings {
+    /// Load settings from `<store_base_dir>/settings.json`.
+    ///
+    /// Flow: read file → parse JSON → fall back to `Settings::default()` on
+    /// any failure (missing file, unreadable, malformed JSON).
+    ///
+    /// Return: always succeeds; never surfaces I/O or parse errors to the caller.
     pub fn load() -> Self {
         let store = super::store::Store::new();
         let path = store.base_dir.join("settings.json");
@@ -58,6 +78,11 @@ impl Settings {
             .unwrap_or_default()
     }
 
+    /// Serialize and write settings to `<store_base_dir>/settings.json`.
+    ///
+    /// Flow: ensure base dir exists → pretty-print JSON → write to disk.
+    ///
+    /// Return: `Err` if the directory can't be created or the write fails.
     pub fn save(&self) -> std::io::Result<()> {
         let store = super::store::Store::new();
         std::fs::create_dir_all(&store.base_dir)?;