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/harness.rs

@@ -1,3 +1,10 @@
+//! Tool-call gating: decides whether a risky tool call is allowed to run
+//! before it executes.
+
+/// Outcome of gating a tool call: whether it's allowed to run.
+///
+/// Why: `Block` carries a reason string for surfacing to the user/log, even
+/// though nothing currently produces `Block` (classify() always allows).
 #[derive(Debug, Clone, PartialEq)]
 pub enum Verdict {
     Allow,
@@ -5,9 +12,20 @@ pub enum Verdict {
     Block(String),
 }
 
+/// Gatekeeper that decides whether a tool call may proceed before execution.
 pub struct Harness;
 
 impl Harness {
+    /// Decide whether a tool call is allowed to execute.
+    ///
+    /// Flow: if the tool isn't flagged risky, allow immediately → otherwise
+    /// defer to `classify`.
+    ///
+    /// Why: `_args` and `_workspace_roots` are accepted for a future
+    /// content-aware classifier but currently unused — `classify` is a
+    /// stub that always allows.
+    ///
+    /// Return: `Verdict::Allow` or `Verdict::Block(reason)`.
     pub fn gate_tool_call(
         tool_name: &str,
         _args: &serde_json::Value,