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/app/mode/settings.rs

@@ -1,5 +1,19 @@
+//! Settings-mode helper logic for the TUI settings overlay.
+//!
+//! Flow: exposes small mutation functions (currently just cycling the
+//! internet access mode) invoked by keybindings while the settings overlay
+//! is active.
+
 use crate::model::settings::{Settings, InternetMode};
 
+/// Advance the internet access mode to the next value in the cycle.
+///
+/// Flow: Off -> ReadOnly -> Full -> Off, wrapping around.
+///
+/// Why: used by a settings-toggle keybinding to step through modes
+/// without needing a dropdown/menu.
+///
+/// Return: nothing; mutates `settings.internet_mode` in place.
 pub fn cycle_internet_mode(settings: &mut Settings) {
     settings.internet_mode = match settings.internet_mode {
         InternetMode::Off => InternetMode::ReadOnly,