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/tool/fs/write.rs

@@ -1,3 +1,5 @@
+//! Tool: `write` — write content to a file, creating parent directories on demand.
+
 use std::fs;
 use serde_json::{json, Value};
 use anyhow::{Result, anyhow};
@@ -7,6 +9,7 @@ use super::super::resolve_path;
 use super::super::check_graduated_checks;
 use super::helpers::arg_str;
 
+/// Tool: write content to a file, auto-creating parent directories as needed.
 pub struct Write;
 
 impl Tool for Write {
@@ -39,6 +42,13 @@ impl Tool for Write {
         })
     }
 
+    /// Write content to a file, creating parent directories as needed.
+    ///
+    /// Flow: validate args (non-empty reason) → resolve path → create parent
+    /// dirs → write file → report byte count (+ optional graduated checks).
+    ///
+    /// Why: requires a non-empty `reason` to discourage stray writes; parent
+    /// directories are created silently so the tool works for new paths.
     fn run(&self, ctx: &ToolCtx, args: &Value) -> Result<String> {
         let rel = arg_str(args, "path")?;
         let content = arg_str(args, "content")?;