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/model/store.rs

@@ -1,6 +1,12 @@
+//! Filesystem layout for zesdex's persistent and scratch data directories.
+
 use std::path::PathBuf;
 use serde::{Deserialize, Serialize};
 
+/// Resolved paths for all data directories zesdex reads from and writes to.
+///
+/// Why: centralizing path computation here means every consumer agrees on
+/// where memory, scratch, session images, and downloads live.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct Store {
     pub base_dir: PathBuf,
@@ -11,6 +17,12 @@ pub struct Store {
 }
 
 impl Store {
+    /// Compute the standard set of zesdex data directory paths.
+    ///
+    /// Flow: OS data dir (or `.local/share` fallback) + "zesdex" → base dir;
+    /// scratch root comes from the OS temp dir instead, since it's disposable.
+    ///
+    /// Why: paths are computed, not created — call `ensure_dirs` before use.
     pub fn new() -> Self {
         let base = dirs::data_dir()
             .unwrap_or_else(|| PathBuf::from(".local/share"))
@@ -25,6 +37,9 @@ impl Store {
         }
     }
 
+    /// Create all store directories (base, memory, scratch, session images, downloads) if missing.
+    ///
+    /// Return: `Err` on the first directory that fails to create.
     pub fn ensure_dirs(&self) -> std::io::Result<()> {
         std::fs::create_dir_all(&self.base_dir)?;
         std::fs::create_dir_all(&self.memory_dir)?;