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/search.rs

@@ -1,3 +1,5 @@
+//! Text search tools: `grep` (line matching) and `glob` (filename pattern matching).
+
 use std::fs;
 use serde_json::{json, Value};
 use anyhow::{Result, anyhow};
@@ -7,6 +9,7 @@ use super::Tool;
 use super::ToolCtx;
 use super::resolve_path;
 
+/// Tool that recursively searches text files under a directory for a literal substring.
 pub struct Grep;
 
 impl Tool for Grep {
@@ -35,6 +38,16 @@ impl Tool for Grep {
         })
     }
 
+    /// Recursively walk the resolved directory and collect matching lines.
+    ///
+    /// Flow: extract `pattern` + `path` → `resolve_path` (workspace-scoped) → bail if
+    ///       missing/not a dir → `ignore::Walk` the tree → for each file, `read_to_string`
+    ///       and substring-match each line → emit `<rel_path>:<line_no>:<text>` rows.
+    ///
+    /// Why: `ignore::Walk` respects `.gitignore` and skips heavy dirs (e.g. `.git/`)
+    /// which is what the agent expects when running in real repos.
+    ///
+    /// Return: "no matches found" if empty, else a header + `path:line:text` rows.
     fn run(&self, ctx: &ToolCtx, args: &Value) -> Result<String> {
         let pattern = args.get("pattern")
             .and_then(|v| v.as_str())
@@ -80,6 +93,7 @@ impl Tool for Grep {
     }
 }
 
+/// Tool that lists files under a directory matching a glob pattern.
 pub struct Glob;
 
 impl Tool for Glob {
@@ -108,6 +122,17 @@ impl Tool for Glob {
         })
     }
 
+    /// Walk the resolved directory and collect entries matching the glob pattern.
+    ///
+    /// Flow: extract pattern + path → `resolve_path` → build a `GlobSet` from the
+    ///       joined absolute pattern → `ignore::Walk` the tree → keep entries that
+    ///       match → sort → join with newlines, appending `/` for directories.
+    ///
+    /// Why: joining the workspace-relative pattern onto the resolved root lets users
+    /// supply familiar glob shapes (`**/*.rs`) while the sandbox still controls the
+    /// boundary.
+    ///
+    /// Return: sorted newline-joined matches; "no files match" sentinel if empty.
     fn run(&self, ctx: &ToolCtx, args: &Value) -> Result<String> {
         let pat_str = args.get("pattern")
             .and_then(|v| v.as_str())