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/view/mod.rs

@@ -1,3 +1,7 @@
+//! Top-level TUI render pipeline: layouts the terminal into chat / input
+//! / status regions, dispatches overlay rendering, and floats toast
+//! notifications over the top-right corner.
+
 pub mod chat;
 pub mod markdown;
 pub mod status;
@@ -11,6 +15,17 @@ use ratatui::widgets::{Block, Borders, Clear, Paragraph, Wrap};
 use ratatui::Frame;
 use theme::Theme;
 
+/// Top-level render entry point called once per TUI frame.
+///
+/// Flow: split the frame into main / input / status regions → if an
+/// overlay is active, render it inside the main region; otherwise render
+/// the chat transcript → always render the input bar and status bar →
+/// overlay toast notifications in the top-right corner.
+///
+/// Why: a single function owns the layout so every state change
+/// re-renders the whole UI from a known template.
+///
+/// Return: nothing; writes directly into `frame`.
 pub fn draw(frame: &mut Frame, state: &crate::app::state::rest::AppStateRest) {
     let area = frame.area();
 
@@ -45,6 +60,18 @@ fn render_main_panel(frame: &mut Frame, area: Rect, state: &crate::app::state::r
     chat::draw_chat(frame, area, state);
 }
 
+/// Render the active modal overlay (Help, Settings, Workflow, Bash, Editor, etc.).
+///
+/// Flow: compute a centered sub-area → clear it to make the rest of the
+/// frame visible behind → match on the Overlay variant to pick the
+/// panel's title, content Lines, and styling → render as a Paragraph or
+/// delegate to a specialized drawer (e.g. `workflow::draw_workflow_panel`).
+///
+/// Why: each Overlay variant has its own data sources (settings,
+/// session_runtime, app_config) and its own visual treatment, so they
+/// are dispatched individually rather than table-driven.
+///
+/// Return: nothing; draws directly into `frame`.
 fn render_overlay(frame: &mut Frame, area: Rect, overlay: crate::app::state::types::Overlay, state: &crate::app::state::rest::AppStateRest) {
     let overlay_area = centered_rect(area, 70, 60);
 
@@ -499,6 +526,20 @@ fn render_overlay(frame: &mut Frame, area: Rect, overlay: crate::app::state::typ
     }
 }
 
+/// Render the bottom input bar including the autocomplete dropdown above it.
+///
+/// Flow: if autocomplete is open and has candidates, draw a borderless
+/// dropdown anchored just above the input bar showing up to 10 candidates
+/// with the current selection highlighted → then render the prompt,
+/// placeholder, and the buffer with a single-character highlight under
+/// the cursor position.
+///
+/// Why: the cursor highlight is drawn by splitting the buffer at
+/// `state.input.cursor` and styling one character (or trailing space)
+/// with the highlight color, since ratatui Paragraph does not expose a
+/// native cursor widget.
+///
+/// Return: nothing; draws directly into `frame` at `area`.
 fn render_input_bar(frame: &mut Frame, area: Rect, state: &crate::app::state::rest::AppStateRest) {
     // Render autocomplete dropdown if visible
     if state.input.autocomplete_visible && !state.input.autocomplete_candidates.is_empty() {