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/bgbash/control.rs

@@ -1,14 +1,41 @@
+//! Global registry of running background bash jobs, and control operations
+//! (output polling, kill) exposed to the rest of the app.
+//!
+//! Flow: a process-wide `Mutex<HashMap<String, BashJob>>` (lazily built via
+//! `OnceLock`) holds every job spawned via `bgbash::job::spawn_bash_job` →
+//! `bash_output` drains new lines for a given job id → `bash_kill` removes
+//! a job from the map and signals its child process.
+//!
+//! Why: a single static map (rather than storing jobs in `AppStateRest`)
+//! lets background jobs outlive the borrow of any particular state mutation
+//! and be looked up by id from tool calls issued at arbitrary points.
+
 use std::collections::HashMap;
 use std::sync::Mutex;
 use std::sync::OnceLock;
 
 use super::job::BashJob;
 
+/// Lazily-initialised, process-wide registry of background bash jobs keyed
+/// by job id.
+///
+/// Return: a reference to the static `Mutex<HashMap<...>>`, created on
+/// first access.
 pub(crate) fn bash_jobs_map() -> &'static Mutex<HashMap<String, BashJob>> {
     static JOBS: OnceLock<Mutex<HashMap<String, BashJob>>> = OnceLock::new();
     JOBS.get_or_init(|| Mutex::new(HashMap::new()))
 }
 
+/// Drain any newly available output lines from a background bash job.
+///
+/// Flow: look up the job by id → repeatedly call `try_read_line()` until it
+/// returns `None` → collect into a Vec.
+///
+/// Why: non-blocking; a job that hasn't produced new output yields no lines
+/// rather than blocking the caller.
+///
+/// Return: `Some(lines)` if at least one new line was read, `None` if the
+/// job doesn't exist, the lock is poisoned, or there was nothing new to read.
 pub fn bash_output(id: &str) -> Option<Vec<String>> {
     let mut map = bash_jobs_map().lock().ok()?;
     let job = map.get_mut(id)?;
@@ -19,6 +46,16 @@ pub fn bash_output(id: &str) -> Option<Vec<String>> {
     if lines.is_empty() { None } else { Some(lines) }
 }
 
+/// Terminate a running background bash job and remove it from the registry.
+///
+/// Flow: remove the job from the map → if it has a valid child PID, send
+/// `SIGTERM` to it (unix only) → return.
+///
+/// Why: removing from the map first means a concurrent lookup can no longer
+/// see the job even if the signal delivery is delayed.
+///
+/// Return: `Ok(())` on success, `Err` if the lock is poisoned or no job
+/// with that id exists.
 pub fn bash_kill(id: &str) -> anyhow::Result<()> {
     let mut map = bash_jobs_map().lock().map_err(|e| anyhow::anyhow!("lock error: {}", e))?;
     let job = map.remove(id);

src/app/bgbash/job.rs

@@ -1,8 +1,24 @@
+//! Background bash job spawning and non-blocking output polling.
+//!
+//! Flow: `spawn_bash_job` forks a detached OS thread that execs the command
+//! via `sh -c`, streams stdout lines back over an `mpsc` channel, and sends
+//! an `__exit:<code>` sentinel when the child terminates → callers poll the
+//! returned `BashJob` with `try_read_line()` to drain output without
+//! blocking the TUI event loop.
+//!
+//! Why: running bash commands on a detached thread with a channel (rather
+//! than synchronously) lets the TUI stay responsive while long-running
+//! shell commands execute in the background.
+
 use std::process::{Command, Stdio};
 use std::sync::mpsc;
 use std::thread;
 use std::io::BufRead;
 
+/// Handle to a bash command running in a detached background thread.
+///
+/// Why: output is streamed over an mpsc channel rather than buffered
+/// synchronously, so the TUI can poll for new lines without blocking.
 pub struct BashJob {
     pub id: String,
     pub child_pid: u32,
@@ -10,6 +26,21 @@ pub struct BashJob {
     pub exit_code: Option<i32>,
 }
 
+/// Spawn a shell command in a background thread and return a handle to it.
+///
+/// Flow: spawn a thread → thread execs `sh -c <command>` with piped
+/// stdout/stderr → thread sends the child PID back over a channel →
+/// thread streams stdout lines to `output_tx` → on exit, sends an
+/// `__exit:<code>` sentinel line.
+///
+/// Why: the PID is sent back before the command finishes so `bash_kill` can
+/// terminate it mid-run; sentinel-prefixed strings (`__error:`, `__exit:`)
+/// let `try_read_line` distinguish control messages from real output on the
+/// same channel without a separate enum.
+///
+/// Return: a `BashJob` with a freshly generated id, the child PID (0 if the
+/// spawn failed before the PID was sent), and the receiving end of the
+/// output channel.
 pub fn spawn_bash_job(command: String) -> BashJob {
     let id = uuid::Uuid::new_v4().to_string();
     let (output_tx, output_rx) = mpsc::channel::<String>();
@@ -57,6 +88,15 @@ pub fn spawn_bash_job(command: String) -> BashJob {
 }
 
 impl BashJob {
+    /// Non-blocking poll for the next output line from the job's channel.
+    ///
+    /// Flow: try_recv the channel → if it's an `__exit:<code>` sentinel,
+    /// record `exit_code` and return `None` instead of surfacing it as
+    /// output → otherwise return the line.
+    ///
+    /// Return: `Some(line)` for real output, `None` if there's nothing
+    /// available yet or the job just finished (exit code recorded as a
+    /// side effect).
     pub fn try_read_line(&mut self) -> Option<String> {
         match self.output_rx.try_recv() {
             Ok(line) => {

src/app/bgbash/mod.rs

@@ -1,2 +1,5 @@
+//! Background bash: run shell commands off the main thread, poll their
+//! output non-blockingly, and terminate them on demand.
+
 pub mod control;
 pub mod job;

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,

src/app/mcp/manager.rs

@@ -1,3 +1,7 @@
+//! MCP server connection management: spawning/talking to stdio child
+//! processes and HTTP endpoints, and adapting their advertised tools to
+//! the crate's `Tool` trait.
+
 use serde_json::{json, Value};
 use serde::{Deserialize, Serialize};
 use std::io::{BufRead, BufReader, Write};
@@ -21,6 +25,8 @@ fn mcp_static_str(s: &str) -> &'static str {
     leaked
 }
 
+/// How an MCP server is reached: a spawned child process talking
+/// newline-delimited JSON-RPC over stdio, or a remote HTTP endpoint.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub enum McpTransport {
     Stdio {
@@ -32,6 +38,7 @@ pub enum McpTransport {
     },
 }
 
+/// A single tool advertised by an MCP server, as returned by `tools/list`.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct McpToolInfo {
     pub name: String,
@@ -39,6 +46,8 @@ pub struct McpToolInfo {
     pub input_schema: Value,
 }
 
+/// A connected MCP server: its transport, advertised tools, and (for stdio)
+/// a live handle to the child process.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct McpServer {
     pub name: String,
@@ -51,6 +60,8 @@ pub struct McpServer {
     pub child_handle: Option<Arc<Mutex<StdioChild>>>,
 }
 
+/// Live handle to an MCP server child process communicating over stdio
+/// via newline-delimited JSON-RPC 2.0.
 #[derive(Debug)]
 pub struct StdioChild {
     stdin: std::process::ChildStdin,
@@ -59,6 +70,18 @@ pub struct StdioChild {
 }
 
 impl StdioChild {
+    /// Send a JSON-RPC request to the child and block for its matching response.
+    ///
+    /// Flow: assign the next request id → write request + newline to stdin →
+    /// loop reading lines from stdout until one has a matching `id` or the
+    /// timeout elapses → return its `result` (or error out on an `error` field).
+    ///
+    /// Why: the child may interleave unrelated/malformed lines, so blank
+    /// lines are skipped and non-matching ids are ignored rather than
+    /// treated as a protocol violation.
+    ///
+    /// Return: the `result` value of the matching response, or `Err` on
+    /// timeout, EOF, JSON-RPC error, or I/O failure.
     pub fn call(&mut self, method: &str, params: Value) -> anyhow::Result<Value> {
         self.next_id += 1;
         let id = self.next_id;
@@ -255,11 +278,14 @@ fn extract_text_content(result: &Value) -> anyhow::Result<String> {
     }))
 }
 
+/// Registry of connected MCP servers and their tools for the current session.
 #[derive(Debug, Clone)]
 pub struct McpManager {
     pub servers: Vec<McpServer>,
 }
 
+/// Adapts a single MCP-advertised tool to the crate's `Tool` trait so it can
+/// be dispatched through the same execution path as built-in tools.
 pub struct McpToolAdapter {
     pub tool_name: String,
     pub server_name: String,
@@ -296,12 +322,22 @@ impl crate::tool::Tool for McpToolAdapter {
 }
 
 impl McpManager {
+    /// Create an empty manager with no connected servers.
     pub fn new() -> Self {
         McpManager {
             servers: Vec::new(),
         }
     }
 
+    /// Flatten all connected servers' tools into a single list of `Tool` trait objects.
+    ///
+    /// Flow: for each server, clone its child handle → wrap each of its
+    /// `McpToolInfo` entries in an `McpToolAdapter` sharing that handle.
+    ///
+    /// Why: the handle is cloned (Arc) per tool so every adapter for a given
+    /// stdio server reuses the same persistent child process/connection.
+    ///
+    /// Return: boxed `Tool` trait objects ready to merge into the harness's tool list.
     pub fn as_tools(&self) -> Vec<Box<dyn crate::tool::Tool>> {
         self.servers.iter().flat_map(|server| {
             let handle = server.child_handle.clone();

src/app/mcp/mod.rs

@@ -1 +1,4 @@
+//! Model Context Protocol (MCP) client: connects to external MCP servers
+//! (stdio or HTTP) and exposes their tools through the crate's `Tool` trait.
+
 pub mod manager;

src/app/mod.rs

@@ -1,3 +1,5 @@
+//! Top-level application module: harness, modes, runtime loop, state,
+//! workflows, subagents, review, background bash, and MCP integration.
 pub mod harness;
 pub mod mode;
 pub mod runtime;

src/app/mode/bash.rs

@@ -1,5 +1,16 @@
+//! Bash mode: handles submitting a shell command from the bash input panel.
+
 use crate::app::state::rest::AppStateRest;
 
+/// Launch a background bash job for the submitted command.
+///
+/// Flow: ignore empty input → spawn the job (fire-and-forget, the job's
+/// output is polled elsewhere via `bgbash::control`) → mark state dirty
+/// so the TUI re-renders.
+///
+/// Why: the returned `BashJob` handle is intentionally dropped — this
+/// function only needs to kick the job off; the job registers itself in
+/// the shared jobs map for later polling.
 pub fn handle_bash_submit(state: &mut AppStateRest, command: String) {
     if !command.is_empty() {
         let _ = crate::app::bgbash::job::spawn_bash_job(command);

src/app/mode/editor.rs

@@ -1,6 +1,11 @@
+//! Editor mode: a minimal in-TUI line editor for viewing/modifying a file,
+//! with bounded undo history.
+
 use crate::app::state::rest::AppStateRest;
 use crate::app::state::types::Overlay;
 
+/// State for the built-in line editor overlay: buffer contents, cursor
+/// position, and a bounded undo stack.
 #[derive(Debug, Clone)]
 pub struct EditorState {
     pub path: String,
@@ -23,6 +28,8 @@ impl Default for EditorState {
 }
 
 impl EditorState {
+    /// Create a fresh editor state for `path`, seeded with existing content
+    /// (or a single empty line for a new file).
     pub fn open(path: String, existing_content: Option<Vec<String>>) -> Self {
         let content = existing_content.unwrap_or_else(|| vec![String::new()]);
         EditorState {
@@ -32,12 +39,20 @@ impl EditorState {
         }
     }
 
+    /// Insert a new empty line immediately after the cursor line.
+    ///
+    /// Why: snapshots content to the undo stack first, matching every other
+    /// mutating method here.
     pub fn insert_line_after(&mut self) {
         self.save_undo();
         let pos = (self.cursor_line + 1).min(self.content.len());
         self.content.insert(pos, String::new());
     }
 
+    /// Push a snapshot of the current content onto the undo stack, capped at 50 entries.
+    ///
+    /// Why: `remove(0)` on overflow bounds memory use at the cost of O(n)
+    /// shifting; the cap (50) keeps that cost negligible in practice.
     fn save_undo(&mut self) {
         self.undo_stack.push(self.content.clone());
         if self.undo_stack.len() > 50 {
@@ -45,6 +60,7 @@ impl EditorState {
         }
     }
 
+    /// Move the cursor down one line, clamping the column to the new line's length.
     pub fn cursor_down(&mut self) {
         if self.cursor_line + 1 < self.content.len() {
             self.cursor_line += 1;
@@ -54,6 +70,7 @@ impl EditorState {
         );
     }
 
+    /// Insert a character at the cursor and advance the cursor past it.
     pub fn insert_char(&mut self, c: char) {
         self.save_undo();
         if let Some(line) = self.content.get_mut(self.cursor_line) {
@@ -62,6 +79,11 @@ impl EditorState {
         }
     }
 
+    /// Delete the character before the cursor (backspace).
+    ///
+    /// Flow: if not at column 0, remove the preceding char on this line →
+    /// otherwise (start of line, not the first line) merge this line into
+    /// the previous one, joining at the old line's end.
     pub fn delete_left(&mut self) {
         self.save_undo();
         if let Some(line) = self.content.get_mut(self.cursor_line) {
@@ -78,11 +100,18 @@ impl EditorState {
         }
     }
 
+    /// Join all lines with `\n` into the full file contents, for saving.
     pub fn as_string(&self) -> String {
         self.content.join("\n")
     }
 }
 
+/// Feed a chunk of typed text into the active editor, translating newlines
+/// and tabs into editor operations.
+///
+/// Flow: no-op if no editor is open → for each char: `\n`/`\r` inserts a
+/// line and moves down, `\t` inserts two spaces, everything else inserts
+/// the char directly → mark state dirty.
 pub fn handle_editor_input(state: &mut AppStateRest, text: String) {
     let editor = &mut state.misc.editor;
     if editor.is_none() {
@@ -108,6 +137,7 @@ pub fn handle_editor_input(state: &mut AppStateRest, text: String) {
     state.dirty = true;
 }
 
+/// Close the editor overlay without saving, clearing editor state.
 pub fn handle_editor_dismiss(state: &mut AppStateRest) {
     state.misc.editor = None;
     state.misc.overlay = Overlay::None;

src/app/mode/effort.rs

@@ -1,3 +1,6 @@
+//! Effort mode: cycles the agent's reasoning effort level, which scales the
+//! LLM's temperature and max_tokens for subsequent turns.
+
 use crate::app::state::rest::AppStateRest;
 
 pub const EFFORT_LEVELS: &[&str] = &["low", "medium", "high", "xhigh", "max"];
@@ -17,15 +20,24 @@ pub fn generation_params(level: usize, base_max_tokens: u32) -> (f32, u32) {
     (temperature, max_tokens.max(256))
 }
 
+/// Return the current effort level index, clamped to a valid `EFFORT_LEVELS` slot.
+///
+/// Why: clamping guards against a stale/out-of-range value in loaded state
+/// (e.g. after `EFFORT_LEVELS` shrinks between versions).
 pub fn current_effort(state: &AppStateRest) -> usize {
     state.misc.effort_level.min(EFFORT_LEVELS.len() - 1)
 }
 
+/// Return the current effort level's display name (e.g. "medium").
 pub fn current_effort_str(state: &AppStateRest) -> &'static str {
     let idx = current_effort(state);
     EFFORT_LEVELS[idx]
 }
 
+/// Advance to the next effort level, wrapping around, and toast the new value.
+///
+/// Flow: compute `(current + 1) % len` → store it → push an info toast with
+/// the new level's label → mark state dirty.
 pub fn cycle_effort(state: &mut AppStateRest) {
     let current = current_effort(state);
     state.misc.effort_level = (current + 1) % EFFORT_LEVELS.len();

src/app/mode/help.rs

@@ -1,3 +1,5 @@
+//! Help mode: static help text and the action that opens/closes the help overlay.
+
 use crate::app::runtime::actions::Action;
 use crate::app::state::types::Overlay;
 
@@ -27,6 +29,12 @@ Slash commands:
   /lesson import    Import lessons
   /clear            Clear transcript";
 
+/// Route an incoming action while the help overlay is open.
+///
+/// Flow: `CloseOverlay` passes through unchanged; any other action is
+/// treated as "open help" (idempotent — re-opens the overlay it's already on).
+///
+/// Return: the `Action` to actually dispatch.
 pub fn handle_help_action(action: &Action) -> Action {
     match action {
         Action::CloseOverlay => Action::CloseOverlay,

src/app/mode/key_input.rs

@@ -1,5 +1,8 @@
+//! Key input mode: raw text capture overlay used for one-off key/text prompts.
+
 use crate::app::state::rest::AppStateRest;
 
+/// Replace the input buffer with the given text and mark state dirty.
 pub fn handle_key_text(state: &mut AppStateRest, text: String) {
     state.input.buffer = text;
     state.dirty = true;

src/app/mode/loading.rs

@@ -1,3 +1,5 @@
+//! Loading mode: transient overlay shown while waiting on an async operation.
+
 use crate::app::state::rest::AppStateRest;
 
 pub const LOADING_MESSAGES: &[&str] = &[
@@ -7,6 +9,7 @@ pub const LOADING_MESSAGES: &[&str] = &[
     "almost done...",
 ];
 
+/// Mark state dirty to force a re-render (e.g. to advance the loading spinner/message).
 pub fn resolve_loading(state: &mut AppStateRest) {
     state.dirty = true;
 }

src/app/mode/mcp.rs

@@ -1,5 +1,11 @@
+//! MCP mode: overlay for connecting to a configured MCP server.
+
 use crate::app::state::rest::AppStateRest;
 
+/// Placeholder entry point for connecting to an MCP server by name.
+///
+/// Why: not yet wired to `McpManager::connect_stdio` — currently just
+/// marks state dirty so the overlay re-renders.
 pub fn connect_mcp(state: &mut AppStateRest, server_name: &str) {
     let _ = server_name;
     state.dirty = true;

src/app/mode/mod.rs

@@ -1,3 +1,6 @@
+//! TUI mode definitions and per-mode input/action handlers, one submodule
+//! per overlay/mode (bash, editor, effort, mcp, quit confirm, rewind, etc.).
+
 use serde::{Deserialize, Serialize};
 
 pub mod bash;
@@ -11,6 +14,8 @@ pub mod rewind;
 pub mod settings;
 pub mod todo;
 
+/// Which input/overlay mode the TUI is currently in; drives both key
+/// routing (`controller/input.rs`) and rendering.
 #[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)]
 pub enum ModeKind {
     Chat,

src/app/mode/quit_confirm.rs

@@ -1,5 +1,11 @@
+//! Quit-confirm mode: the "are you sure?" overlay shown before exiting.
+
 use crate::app::runtime::actions::Action;
 
+/// Translate the user's yes/no answer on the quit-confirm overlay into an action.
+///
+/// Return: `Action::ForceQuit` if confirmed, otherwise `Action::CloseOverlay`
+/// to dismiss the prompt without quitting.
 pub fn handle_quit_confirm(yes: bool) -> Action {
     if yes {
         Action::ForceQuit

src/app/mode/rewind.rs

@@ -1,3 +1,6 @@
+//! Rewind mode: restores a file to a pre-edit snapshot stored in the
+//! session's SQLite blob store.
+
 use crate::app::state::rest::AppStateRest;
 use sha2::Digest;
 

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,

src/app/mode/todo.rs

@@ -1,6 +1,19 @@
+//! Todo-mode helper logic for the TUI todo-list overlay.
+//!
+//! Flow: exposes the toggle handler invoked by a keybinding to show/hide
+//! the todo overlay.
+
 use crate::app::state::rest::AppStateRest;
 use crate::app::state::types::Overlay;
 
+/// Toggle the todo-list overlay open or closed.
+///
+/// Flow: if the todo overlay is currently shown, hide it (set to `Overlay::None`);
+/// otherwise show it.
+///
+/// Why: marks state dirty so the TUI re-renders on the next frame.
+///
+/// Return: nothing; mutates `state.misc.overlay` and `state.dirty` in place.
 pub fn handle_todo_toggle(state: &mut AppStateRest) {
     if state.misc.overlay == Overlay::Todo {
         state.misc.overlay = Overlay::None;

src/app/mode/workflow.rs

@@ -1,6 +1,21 @@
+//! Workflow-mode helper logic for the TUI workflow overlay.
+//!
+//! Flow: exposes a dismiss handler invoked by a keybinding to close the
+//! workflow overlay, and a status query used elsewhere to check whether
+//! it is currently showing.
+
 use crate::app::state::rest::AppStateRest;
 use crate::app::state::types::Overlay;
 
+/// Close the workflow overlay if it is the currently active overlay.
+///
+/// Flow: check `state.misc.overlay == Overlay::Workflow`, reset to `Overlay::None`
+/// if so, then mark state dirty regardless.
+///
+/// Why: no-ops safely if another overlay is showing, so it can be called
+/// unconditionally from a dismiss keybinding.
+///
+/// Return: nothing; mutates `state.misc.overlay` and `state.dirty` in place.
 pub fn handle_workflow_dismiss(state: &mut AppStateRest) {
     if state.misc.overlay == Overlay::Workflow {
         state.misc.overlay = Overlay::None;
@@ -8,6 +23,11 @@ pub fn handle_workflow_dismiss(state: &mut AppStateRest) {
     state.dirty = true;
 }
 
+/// Report whether the workflow overlay is currently displayed.
+///
+/// Flow: compare `state.misc.overlay` against `Overlay::Workflow`.
+///
+/// Return: `"active"` if the workflow overlay is shown, `"idle"` otherwise.
 pub fn workflow_status(state: &AppStateRest) -> &str {
     if state.misc.overlay == Overlay::Workflow {
         "active"

src/app/review/mod.rs

@@ -1,3 +1,5 @@
+//! Adaptive quality-review triggering, build/test probing, staleness
+//! sweeps for stored lessons, and the pending-lesson approval workflow.
 use std::process::Command;
 use crate::app::state::rest::AppStateRest;
 use crate::app::state::runtime::TurnEvent;
@@ -7,6 +9,7 @@ use crate::app::subagent::engine::run_subagent;
 use crate::app::subagent::spawn::AgentDefinition;
 use serde::{Deserialize, Serialize};
 
+/// How much trust a lesson's origin/verification warrants.
 #[derive(Debug, Clone, Serialize, Deserialize, PartialEq)]
 pub enum Confidence {
     Human,
@@ -15,6 +18,7 @@ pub enum Confidence {
     Auto,
 }
 
+/// Where a lesson sits in its life cycle, from freshly written to superseded.
 #[derive(Debug, Clone, Serialize, Deserialize, PartialEq)]
 pub enum LessonLifecycle {
     New,
@@ -24,12 +28,14 @@ pub enum LessonLifecycle {
     Superseded,
 }
 
+/// Whether a lesson applies to the current project only or globally.
 #[derive(Debug, Clone, Serialize, Deserialize, PartialEq)]
 pub enum LessonScope {
     Project,
     Global,
 }
 
+/// Records who/what produced a lesson and in which session/turn.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct Provenance {
     pub session_turn: String,
@@ -37,6 +43,8 @@ pub struct Provenance {
     pub reviewer: Origin,
 }
 
+/// A single learned fact/pattern surfaced by a review, prior to being
+/// written to persistent memory.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct Lesson {
     pub name: String,
@@ -49,6 +57,18 @@ pub struct Lesson {
     pub provenance: Provenance,
 }
 
+/// Decide whether an adaptive quality review should fire for this turn.
+///
+/// Flow: only `Origin::Main` turns are eligible → require review enabled
+/// in settings → fire every 5th edit unconditionally → otherwise, once
+/// `consecutive_empty_reviews` reaches `adaptive_review_max_skip` (min 2),
+/// fire on an exponentially growing skip interval (2^n, capped at 2^10)
+/// to avoid reviewing every single edit once reviews keep coming back empty.
+///
+/// Why: balances review usefulness against wasted subagent calls when
+/// reviews consistently find nothing.
+///
+/// Return: `true` if a review should be triggered this turn.
 pub fn should_trigger_review(state: &AppStateRest, origin: Origin) -> bool {
 
     if origin != Origin::Main {
@@ -75,6 +95,7 @@ pub fn should_trigger_review(state: &AppStateRest, origin: Origin) -> bool {
     }
     false
 }
+/// Outcome of running a build/test probe command against a workspace.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct ProbeResult {
     pub command: String,
@@ -82,6 +103,21 @@ pub struct ProbeResult {
     pub output: String,
     pub timed_out: bool,
 }
+
+/// Run a build/test verification command in the first workspace root and
+/// capture its outcome, to back a review with a real pass/fail signal.
+///
+/// Flow: pick the first workspace → resolve the verify command (explicit
+/// override or auto-detected via `resolve_verify_command`) → spawn it →
+/// poll `try_wait` in a loop, killing the child if `timeout_ms` elapses →
+/// capture combined stdout+stderr (truncated) on completion.
+///
+/// Why: polling instead of a blocking wait lets the timeout be enforced
+/// without spawning a watcher thread.
+///
+/// Return: `None` if no workspace exists, no command could be resolved,
+/// or the process failed to spawn/poll; otherwise `Some(ProbeResult)`
+/// describing pass/fail/timeout and truncated output.
 pub fn probe_build_test(workspaces: &[std::path::PathBuf], verify_command: Option<&str>, timeout_ms: u64) -> Option<ProbeResult> {
     let probe_dir = workspaces.first()?;
     let cmd = resolve_verify_command(probe_dir, verify_command)?;
@@ -131,6 +167,19 @@ pub fn probe_build_test(workspaces: &[std::path::PathBuf], verify_command: Optio
     }
 }
 
+/// Determine the shell command to build/test a workspace, auto-detecting
+/// the project type from marker files when no override is given.
+///
+/// Flow: use `override_cmd` verbatim if non-empty → otherwise probe for
+/// language/tool marker files (Cargo.toml, go.mod, package.json, etc.)
+/// in priority order and return that ecosystem's conventional test/build
+/// command.
+///
+/// Why: covers a broad set of ecosystems so review probing works without
+/// per-project configuration in the common case.
+///
+/// Return: `Some(command)` if a command could be determined, `None` if
+/// no marker files matched (e.g. plain Python project with no test dir).
 fn resolve_verify_command(probe_dir: &std::path::Path, override_cmd: Option<&str>) -> Option<String> {
     if let Some(cmd) = override_cmd {
         if !cmd.trim().is_empty() {
@@ -227,6 +276,10 @@ fn resolve_verify_command(probe_dir: &std::path::Path, override_cmd: Option<&str
     None
 }
 
+/// Truncate a string to at most `max` characters, appending a marker if cut.
+///
+/// Return: the original string if short enough, otherwise the first `max`
+/// characters plus `"... (truncated)"`.
 fn truncate_output(s: &str, max: usize) -> String {
     if s.len() <= max {
         s.to_string()
@@ -237,6 +290,22 @@ fn truncate_output(s: &str, max: usize) -> String {
     }
 }
 
+/// Spawn a background quality-review subagent for the current session.
+///
+/// Flow: build a "quality-reviewer" subagent context → probe build/test
+/// status via `probe_build_test` to give the reviewer a real pass/fail
+/// signal → compose a system prompt embedding the probe result and lesson
+/// tagging instructions → spawn a thread running `run_subagent` → on
+/// completion, push a `TurnEvent::SystemNote` with the verdict's first
+/// line (or error) → push an "in progress" toast immediately.
+///
+/// Why: runs on a plain OS thread (not tokio) so it doesn't block the
+/// async event loop; communicates its result back via `turn_events`
+/// rather than a channel receiver (the `_rx` half is intentionally unused).
+///
+/// Return: `Ok(())` once the review has been kicked off; errors only
+/// propagate from constructing the subagent context, not from the review
+/// itself (that failure is reported via a `SystemNote` instead).
 pub fn trigger_review(state: &mut AppStateRest) -> anyhow::Result<()> {
     let def = AgentDefinition::new(
         "quality-reviewer".to_string(),
@@ -310,6 +379,14 @@ pub fn trigger_review(state: &mut AppStateRest) -> anyhow::Result<()> {
 
 const STALE_AFTER_DAYS: i64 = 60;
 
+/// Flag memory entries as stale if they haven't been updated recently.
+///
+/// Flow: list all memory files → for each, read it → if `updated_at` is
+/// older than `STALE_AFTER_DAYS` and it isn't already flagged, set
+/// `lifecycle = "stale"` and write it back → collect flagged names.
+///
+/// Return: names of newly-flagged memories, or an I/O error from
+/// `mem.write`.
 pub fn run_staleness_sweep(memory_dir: &std::path::Path) -> std::io::Result<Vec<String>> {
     let mut flagged = Vec::new();
     let names = crate::model::memory::Memory::list(memory_dir);
@@ -327,6 +404,14 @@ pub fn run_staleness_sweep(memory_dir: &std::path::Path) -> std::io::Result<Vec<
     Ok(flagged)
 }
 
+/// Run the staleness sweep at most once every 10 minutes, notifying via toast.
+///
+/// Flow: skip if less than 600,000ms since `last_staleness_sweep_ms` →
+/// otherwise update the timestamp and run `run_staleness_sweep`, pushing
+/// an info toast listing flagged lessons if any were found.
+///
+/// Why: rate-limited so the sweep (a file read/write per memory) doesn't
+/// run on every event-loop tick.
 pub fn maybe_run_staleness_sweep(state: &mut AppStateRest) {
     let now = chrono::Utc::now().timestamp_millis();
     if now.saturating_sub(state.misc.last_staleness_sweep_ms) < 600_000 {
@@ -343,6 +428,8 @@ pub fn maybe_run_staleness_sweep(state: &mut AppStateRest) {
     }
 }
 
+/// A lesson awaiting confirmation before being committed to memory,
+/// optionally auto-resolving after a grace period.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct PendingLesson {
     pub lesson: Lesson,
@@ -350,6 +437,10 @@ pub struct PendingLesson {
     pub auto_resolve: bool,
 }
 
+/// Load the session's pending-lessons queue from disk.
+///
+/// Return: the parsed list, or an empty `Vec` if the file is missing or
+/// fails to parse.
 pub fn load_pending_lessons(session_dir: &std::path::Path) -> Vec<PendingLesson> {
     let path = session_dir.join("pending_lessons.json");
     std::fs::read_to_string(&path)
@@ -358,12 +449,28 @@ pub fn load_pending_lessons(session_dir: &std::path::Path) -> Vec<PendingLesson>
         .unwrap_or_default()
 }
 
+/// Write the session's pending-lessons queue to disk as pretty JSON.
+///
+/// Return: `Ok(())`, or an I/O error from writing the file.
 pub fn save_pending_lessons(session_dir: &std::path::Path, pending: &[PendingLesson]) -> std::io::Result<()> {
     let path = session_dir.join("pending_lessons.json");
     let data = serde_json::to_string_pretty(pending)?;
     std::fs::write(&path, data)
 }
 
+/// Commit any auto-resolvable pending lessons whose grace period has
+/// elapsed, and persist the remaining queue.
+///
+/// Flow: load pending lessons → partition into those eligible to commit
+/// (`auto_resolve` and older than the 5s grace window) vs. still pending
+/// → write eligible lessons as new `Memory` entries with `lifecycle:
+/// "active"` → save the remaining (unresolved) queue back to disk.
+///
+/// Why: the grace window gives the user a brief window to reject an
+/// auto-resolving lesson via `resolve_pending_lesson` before it commits.
+///
+/// Return: the still-pending lessons (post-commit), or an I/O error from
+/// writing memory files or the queue.
 pub fn process_pending_lessons(session_dir: &std::path::Path, memory_dir: &std::path::Path) -> std::io::Result<Vec<PendingLesson>> {
     let pending = load_pending_lessons(session_dir);
     let now = chrono::Utc::now().timestamp_millis();
@@ -399,6 +506,17 @@ pub fn process_pending_lessons(session_dir: &std::path::Path, memory_dir: &std::
     save_pending_lessons(session_dir, &remaining)?;
     Ok(remaining)
 }
+/// Manually resolve a single pending lesson by name: commit it to memory
+/// or discard it.
+///
+/// Flow: load the queue → find the lesson matching `lesson_name` →
+/// if `keep` is true, write it as an active `Memory` entry; either way
+/// remove it from the queue → save the remaining queue.
+///
+/// Why: lets the user (or UI action) override a pending lesson's fate
+/// before/without waiting for the auto-resolve grace window.
+///
+/// Return: `Ok(())`, or an I/O error from writing the memory file or queue.
 pub fn resolve_pending_lesson(
     session_dir: &std::path::Path,
     memory_dir: &std::path::Path,

src/app/runtime/actions/mod.rs

@@ -1,3 +1,21 @@
+//! The `Action` enum and its single dispatcher, `apply_action` — the
+//! chokepoint through which every key input, streaming event, and async
+//! background-thread result mutates `AppStateRest`.
+//!
+//! Flow: controllers/subagent threads construct `Action` values → the event
+//! loop calls `apply_action(&mut state, action)` → for turn-producing
+//! actions (`SubmitInput`), `spawn_turn` is kicked off on a background OS
+//! thread which drives `run_agent_turn` (stream to the LLM, gate and
+//! execute tool calls via `Harness`, archive messages to SQLite, log edits)
+//! and pushes `TurnEvent`s onto a shared queue → on the next `Tick`, queued
+//! `TurnEvent`s are drained back into `AppStateRest` (transcript, toasts,
+//! usage counters).
+//!
+//! Why: keeping all state mutation behind one function means callers only
+//! need to know how to *produce* actions, not how to update state safely;
+//! running turns on plain OS threads (rather than blocking the main loop)
+//! keeps the TUI responsive while the LLM streams.
+
 use std::collections::VecDeque;
 
 use crate::app::harness::Verdict;
@@ -9,11 +27,14 @@ use crate::app::state::runtime::TurnEvent;
 use crate::app::state::types::{Origin, Overlay, Toast, ToastKind};
 use crate::dto::chat::message::{ChatMessage, Role};
 
-// Step bounds intentionally left unbounded (usize::MAX) so the agent can
-// continue across as many turns as needed. Each iteration still honours
-// `tc.abort_flag` and the per-call LLM timeout, so a runaway loop is
-// observable and cancellable from the UI.
-
+/// A single, well-typed event in the app — produced by key input, the
+/// streaming pipeline, or subagent threads — that mutates `AppStateRest`
+/// when applied via `apply_action`.
+///
+/// Step bounds intentionally left unbounded (usize::MAX) so the agent can
+/// continue across as many turns as needed. Each iteration still honours
+/// `tc.abort_flag` and the per-call LLM timeout, so a runaway loop is
+/// observable and cancellable from the UI.
 #[derive(Debug, Clone)]
 pub enum Action {
     ForceQuit,
@@ -63,6 +84,18 @@ pub enum Action {
     AbortTurn,
 }
 
+/// Apply an `Action` to the application state.
+///
+/// Flow: pattern-match the variant → mutate `state` (input buffer, scroll
+/// position, overlay, transcript, runtime, toasts, dirty flag, etc.) →
+/// for `Tick`, also drain queued `TurnEvent`s and run periodic side jobs
+/// (staleness sweep, pending-lesson commit).
+///
+/// Why: the single chokepoint that turns every typed key and async event
+/// into a state change, so callers (controllers, subagent threads) only
+/// need to know how to *produce* actions.
+///
+/// Return: nothing; `state` is mutated in place.
 pub fn apply_action(state: &mut AppStateRest, action: Action) {
     match action {
         Action::ForceQuit => {
@@ -449,6 +482,19 @@ pub fn apply_action(state: &mut AppStateRest, action: Action) {
     }
 }
 
+/// Spawn a background thread that runs one full LLM turn.
+///
+/// Flow: check that no turn is currently in-flight → bail if so →
+/// collect messages and config from state → determine API key (from
+/// settings, env var, or default) → resolve generation params from
+/// the current effort level → collect all tools (built-in + MCP) →
+/// build `TurnCtx` → spawn a thread running `run_agent_turn` →
+/// on any error, push a `TurnEvent::Error` → clear the in-flight flag
+/// when the thread exits.
+///
+/// Why: runs on a plain OS thread so the async event loop stays responsive.
+///
+/// Return: nothing; results flow through `state.turn_events`.
 fn spawn_turn(state: &AppStateRest) {
     let in_flight = if let Ok(guard) = state.turn_in_flight.lock() {
         *guard
@@ -532,6 +578,7 @@ fn spawn_turn(state: &AppStateRest) {
     });
 }
 
+/// Context bundle passed to `run_agent_turn` on its background thread.
 struct TurnCtx {
     client: crate::service::provider::LlmClient,
     tdefs: Vec<crate::dto::provider::request::ToolDef>,
@@ -547,6 +594,14 @@ struct TurnCtx {
     abort_flag: std::sync::Arc<std::sync::atomic::AtomicBool>,
 }
 
+/// Build an ASCII tree of the workspace directory structure for the
+/// system prompt, so the LLM can see the file layout.
+///
+/// Flow: for each root, walk using `ignore::WalkBuilder` (respecting
+/// `.gitignore` and hidden files) → prefix `[DIR]` for directories →
+/// truncate after 1000 entries.
+///
+/// Return: a formatted string with one entry per line.
 fn generate_workspace_tree(roots: &[std::path::PathBuf]) -> String {
     let mut out = String::new();
     out.push_str("Current Workspace Directory Structure:\n");
@@ -575,6 +630,11 @@ fn generate_workspace_tree(roots: &[std::path::PathBuf]) -> String {
     out
 }
 
+/// Persist a `ChatMessage` to the SQLite message log, if a database
+/// connection is available.
+///
+/// Flow: if `db` is `Some`, lock the mutex and call `insert_message`.
+/// Errors are silently ignored.
 fn archive_message(db: &Option<std::sync::Arc<std::sync::Mutex<rusqlite::Connection>>>, session_id: &str, msg: &ChatMessage) {
     if let Some(ref arc) = db {
         if let Ok(conn) = arc.lock() {
@@ -583,6 +643,28 @@ fn archive_message(db: &Option<std::sync::Arc<std::sync::Mutex<rusqlite::Connect
     }
 }
 
+/// Execute one full agent turn: stream the conversation to the LLM,
+/// handle tool calls, and loop until the LLM produces a non-tool response
+/// or runs out of unfinished todo items.
+///
+/// Flow: build system prompt with workspace tree → optionally shape
+/// (compact) messages via `shortsend` → call `chat_with_tools_streaming`
+/// with a callback that pushes `StreamStart`, `StreamToken`, `Reasoning`,
+/// and `Usage` events → on streaming success, handle tool calls (gated
+/// through `Harness::gate_tool_call`) or unwrap the final assistant
+/// message → check for unfinished todo.md tasks (auto-retry with a
+/// system message if any remain) → finalise with `Done` and an `edits`
+/// SystemNote.
+///
+/// On streaming failure: retry once with a non-streaming call → if that
+/// also fails and there are unfinished tasks, sleep 5s and loop back;
+/// otherwise return the error.
+///
+/// Why: non-streaming fallback handles flaky connections without aborting
+/// the turn; todo.md polling lets the agent self-direct toward completeness.
+///
+/// Return: `Ok(())` on successful completion, or an error from the LLM
+/// API after retries are exhausted.
 fn run_agent_turn(
     tc: TurnCtx,
     messages: &[ChatMessage],
@@ -836,6 +918,20 @@ fn run_agent_turn(
     Ok(())
 }
 
+/// Execute a single tool call: find the tool by name, snapshot the file
+/// (if write/edit) for rewind, run the tool, log an `EditLogEntry` for
+/// write/edit, and return the output.
+///
+/// Flow: iterate tools → match by name → for write/edit, snapshot the
+/// pre-existing file content into the blob store → call `tool.run()` →
+/// for write/edit, compute SHA-256 of the new content and append an
+/// `EditLogEntry` → return the tool output string.
+///
+/// Why: snapshots enable the rewind feature to restore previous content
+/// after a write/edit.
+///
+/// Return: the tool's stdout string, or an error if no matching tool was
+/// found or the tool run itself failed.
 #[allow(clippy::too_many_arguments)]
 fn execute_one_tool(
     tools: &[Box<dyn crate::tool::Tool>],
@@ -910,6 +1006,15 @@ fn execute_one_tool(
     anyhow::bail!("tool not found: {}", name)
 }
 
+/// Optionally push a review-available toast at the end of a turn that
+/// performed edits.
+///
+/// Flow: skip if review is disabled → skip if `edit_count` is zero →
+/// push an info toast listing the number of modified files.
+///
+/// Why: does not launch the review itself (that happens inside
+/// `should_trigger_review` on `Tick`), only informs the user that
+/// a review has material to examine.
 fn maybe_trigger_review(state: &mut AppStateRest) {
     if !state.settings.review_enabled {
         return;
@@ -928,6 +1033,13 @@ fn maybe_trigger_review(state: &mut AppStateRest) {
     ));
 }
 
+/// Persist the current session metadata and conversation to disk.
+///
+/// Flow: build a `Session` object → save its metadata → write
+/// `rt.messages` as JSON to the conversation file → errors are silently
+/// ignored.
+///
+/// Why: called on `ForceQuit` so the session can be resumed later.
 fn save_current_session(state: &AppStateRest) {
     let base = state.store_base_dir();
     let session = crate::model::session::Session::new(
@@ -943,6 +1055,20 @@ fn save_current_session(state: &AppStateRest) {
     }
 }
 
+/// Run a browser-based OAuth PKCE flow for the given provider.
+///
+/// Flow: look up config by provider name ("zen"/"opencode", "openai",
+/// or a custom provider via env vars) → bind a loopback server → generate
+/// a PKCE code verifier and challenge → build the authorisation URL →
+/// wait for the redirect code on the loopback server (with a 120s timeout)
+/// → exchange the code for a token → save the token to
+/// `~/.config/zesdex/oauth_{provider}.json`.
+///
+/// Why: the `webbrowser::open` call is currently commented out; the user
+/// must open the auth URL manually until that line is reinstated.
+///
+/// Return: a success message on completion, or an error if the flow fails
+/// at any step.
 fn run_oauth_flow(provider: &str) -> anyhow::Result<String> {
     use crate::service::oauth::manager::{OAuthConfig, OAuthManager};
     use crate::service::oauth::loopback::LoopbackServer;
@@ -1013,6 +1139,11 @@ fn run_oauth_flow(provider: &str) -> anyhow::Result<String> {
     Ok(format!("Successfully authenticated with {}.", provider))
 }
 
+/// Generate `n` pseudo-random bytes from the current sub-second timestamp.
+///
+/// Why: avoids pulling in a full RNG crate for the OAuth state token;
+/// sufficient for a nonce that only needs to be unpredictable over the
+/// lifetime of a single OAuth flow.
 fn rand_bytes(n: usize) -> Vec<u8> {
     use std::time::{SystemTime, UNIX_EPOCH};
     let seed = SystemTime::now().duration_since(UNIX_EPOCH).unwrap_or_default().subsec_nanos();

src/app/runtime/commands.rs

@@ -1,7 +1,18 @@
+//! Maps parsed `/` slash commands into one or more `Action` variants
+//! that `apply_action` can process.
 use crate::controller::command::Command;
 use crate::app::runtime::actions::Action;
 use crate::app::state::types::Overlay;
 
+/// Convert a parsed `Command` into the corresponding sequence of `Action`s.
+///
+/// Flow: match each `Command` variant to its handler — most produce a
+/// single `Action` (open an overlay, dispatch an OAuth flow, open the
+/// editor, etc.); some produce an `Action::SystemNote` for errors or
+/// informational responses.
+///
+/// Return: a `Vec<Action>` (always non-empty) to be applied sequentially
+/// by `apply_action`.
 pub fn apply_command(command: Command) -> Vec<Action> {
     match command {
         Command::Help => {

src/app/runtime/event_loop/mod.rs

@@ -1,3 +1,5 @@
+//! Adaptive poll-rate event loop: polls faster for IDLE_THRESHOLD_MS
+//! after any activity, then slows down to conserve CPU.
 use std::collections::VecDeque;
 use std::time::{Duration, Instant};
 
@@ -7,12 +9,15 @@ const FAST_POLL_MS: u64 = 8;
 const SLOW_POLL_MS: u64 = 100;
 const IDLE_THRESHOLD_MS: u64 = 500;
 
+/// Tracks whether the app has been active vs idle to adjust the TUI poll
+/// rate, balancing responsiveness against CPU usage.
 pub struct EventLoop {
     last_activity: Instant,
     fast_poll_until: Option<Instant>,
 }
 
 impl EventLoop {
+    /// Create an `EventLoop` with the current instant as the last activity.
     pub fn new() -> Self {
         EventLoop {
             last_activity: Instant::now(),
@@ -20,6 +25,10 @@ impl EventLoop {
         }
     }
 
+    /// Return the appropriate polling delay based on activity state.
+    ///
+    /// Flow: if `fast_poll_until` is set and the deadline hasn't expired,
+    /// return `FAST_POLL_MS`; otherwise return `SLOW_POLL_MS`.
     pub fn poll_interval(&self) -> Duration {
         if let Some(fast_until) = self.fast_poll_until {
             if Instant::now() < fast_until {
@@ -29,15 +38,21 @@ impl EventLoop {
         Duration::from_millis(SLOW_POLL_MS)
     }
 
+    /// Mark the current time as the last activity and arm the fast-poll
+    /// window for the next `IDLE_THRESHOLD_MS`.
     pub fn mark_active(&mut self) {
         self.last_activity = Instant::now();
         self.fast_poll_until = Some(Instant::now() + Duration::from_millis(IDLE_THRESHOLD_MS));
     }
 
+    /// Return `true` if the app has been idle for more than `IDLE_THRESHOLD_MS`.
     pub fn is_idle(&self) -> bool {
         self.last_activity.elapsed().as_millis() as u64 > IDLE_THRESHOLD_MS
     }
 
+    /// Drain all pending `TurnEvent`s from the shared mutex queue.
+    ///
+    /// Return: a `Vec` of all events that were in the queue (may be empty).
     pub fn drain_events(
         events: &std::sync::Mutex<VecDeque<TurnEvent>>,
     ) -> Vec<TurnEvent> {

src/app/runtime/mod.rs

@@ -1,3 +1,5 @@
+//! Runtime layer: action dispatch, slash commands, short-send handling,
+//! and the LLM streaming pipeline.
 pub mod actions;
 pub mod commands;
 pub mod shortsend;

src/app/runtime/shortsend.rs

@@ -1,9 +1,20 @@
+//! Short-send / message shaping: compacts long conversation histories so
+//! they fit within the provider's context window before being sent to the
+//! LLM API.
 use crate::dto::chat::message::ChatMessage;
 
 const MAX_WIRE_TOKENS: usize = 2_000_000;
 const MIN_MESSAGES_BEFORE_SHAPE: usize = 20;
 const ENGAGE_HYSTERESIS: usize = 5;
 
+/// Decide whether the message list should be shaped (compacted) before
+/// sending to the LLM.
+///
+/// Flow: skip shaping if fewer than `MIN_MESSAGES_BEFORE_SHAPE` messages
+/// → once past that threshold, use hysteresis (require 5 more messages
+/// before re-engaging if shaping is currently active) to avoid oscillation.
+///
+/// Return: `true` if shaping should be applied.
 pub fn should_shape(total_messages: usize, prev_shaped: bool) -> bool {
     if total_messages < MIN_MESSAGES_BEFORE_SHAPE {
         return false;
@@ -16,6 +27,19 @@ pub fn should_shape(total_messages: usize, prev_shaped: bool) -> bool {
     total_messages >= threshold
 }
 
+/// Compact a long message list by dropping middle messages and inserting
+/// a summary placeholder.
+///
+/// Flow: if the estimated token count is within budget, return messages
+/// unchanged → otherwise keep the system message and the most recent
+/// messages (up to `MAX_WIRE_TOKENS / 200` of them) with a `[prior
+/// conversation compacted]` system message in between.
+///
+/// Why: keeps context-size overhead roughly constant regardless of
+/// session length.
+///
+/// Return: a new Vec<ChatMessage> that preserves the first message and
+/// the tail.
 pub fn shape_messages(messages: &[ChatMessage], token_count: usize) -> Vec<ChatMessage> {
     if token_count <= MAX_WIRE_TOKENS || messages.len() < 10 {
         return messages.to_vec();

src/app/runtime/stream/mod.rs

@@ -1,9 +1,12 @@
+//! SSE stream parser: converts SSE- or JSON-chunked LLM responses into
+//! typed `StreamEvent` variants (tokens, reasoning, tool calls, usage, done).
 pub mod turn;
 pub mod tools;
 
 use serde::{Deserialize, Serialize};
 use serde_json::Value;
 
+/// One atomic event extracted from an LLM streaming response stream.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub enum StreamEvent {
     Token(String),
@@ -23,6 +26,8 @@ pub enum StreamEvent {
     Error(String),
 }
 
+/// Buffered SSE frame parser that accumulates raw `data:` lines and
+/// flushes a `StreamEvent` on each blank-line boundary.
 pub struct SseParser {
     buffer: String,
     event_type: Option<String>,
@@ -30,6 +35,7 @@ pub struct SseParser {
 }
 
 impl SseParser {
+    /// Create a new parser with an empty buffer.
     pub fn new() -> Self {
         SseParser {
             buffer: String::new(),
@@ -38,6 +44,17 @@ impl SseParser {
         }
     }
 
+    /// Feed a raw SSE chunk and produce any completed events.
+    ///
+    /// Flow: append chunk to buffer → scan for '\n' → strip '\r' → on
+    /// blank line, call `flush_event` to parse the accumulated data →
+    /// on `event:` line, store the event type → on `data:` line, append
+    /// to data accumulator → continue until buffer exhausted.
+    ///
+    /// Edge case: a chunk may split mid-line; the remainder stays in the
+    /// buffer for the next `feed()` call.
+    ///
+    /// Return: all `StreamEvent`s completed by this chunk.
     pub fn feed(&mut self, chunk: &str) -> Vec<StreamEvent> {
         self.buffer.push_str(chunk);
         let mut events = Vec::new();
@@ -57,6 +74,19 @@ impl SseParser {
         events
     }
 
+    /// Flush the current buffered `data:` lines as one or more `StreamEvent`s.
+    ///
+    /// Flow: join data lines → handle `[DONE]` sentinel → JSON-parse →
+    /// emit `Usage` if a usage object is present → else match `event_type`
+    /// ("message.stop", "message.delta", etc.) → extract content,
+    /// reasoning, tool-call deltas, or finish-reason from the delta
+    /// structure (supporting both Anthropic-style top-level delta and
+    /// OpenAI-style `choices` array).
+    ///
+    /// Why: dual-format support in one method avoids a separate
+    /// provider-specific parsing layer.
+    ///
+    /// Return: 0, 1, or more `StreamEvent`s from the flushed frame.
     fn flush_event(&mut self) -> Vec<StreamEvent> {
         let data = self.data_lines.join("\n");
         self.data_lines.clear();
@@ -179,6 +209,13 @@ impl SseParser {
 /// Fallback parser for providers that send bare JSON chunks instead of SSE-framed
 /// `data: ...` lines. Not used by the `SseParser` streaming path (which handles
 /// standard SSE framing directly), kept for providers/tests that feed raw chunks.
+///
+/// Flow: parse `data` as JSON → extract first `choices[0].delta` →
+/// return a `Token`, `Reasoning`, `Done`, or `ToolCallDelta` event based
+/// on the fields present.
+///
+/// Return: `Some(StreamEvent)` if the chunk contained recognisable
+/// content, `None` otherwise.
 #[allow(dead_code)]
 pub fn parse_stream_chunk(data: &str) -> Option<StreamEvent> {
     let value: Value = serde_json::from_str(data).ok()?;

src/app/runtime/stream/tools/mod.rs

@@ -1,3 +1,16 @@
+//! Standalone accumulator for streamed tool-call deltas.
+//!
+//! Flow: `ToolCallAccumulator::add_delta` is fed incremental `(index, id,
+//! name, arguments_delta)` chunks as they arrive over SSE → grows its
+//! internal `Vec<ParsedToolCall>` as needed → `is_complete` reports once
+//! every accumulated call has both a name and arguments.
+//!
+//! Why: mirrors the accumulation logic built into `StreamedTurn::apply_event`
+//! but as an independent, reusable type for callers that want to track
+//! tool-call deltas without a full `StreamedTurn` (e.g. a lighter-weight
+//! preview). Currently unused (`#[allow(dead_code)]`), kept for that future
+//! use case.
+
 use super::turn::ParsedToolCall;
 use serde_json::{json, Value};
 
@@ -11,10 +24,15 @@ pub struct ToolCallAccumulator {
 
 #[allow(dead_code)]
 impl ToolCallAccumulator {
+    /// Construct an empty accumulator with no tool calls tracked yet.
+    ///
+    /// Return: a fresh `ToolCallAccumulator`.
     pub fn new() -> Self {
         ToolCallAccumulator { calls: Vec::new() }
     }
 
+    /// Append a delta to the tool call at the given index, growing the
+    /// calls vector if needed.
     pub fn add_delta(
         &mut self,
         index: usize,
@@ -44,18 +62,23 @@ impl ToolCallAccumulator {
         tc.arguments.push_str(arguments_delta);
     }
 
+    /// Borrow the accumulated tool calls.
     pub fn calls(&self) -> &[ParsedToolCall] {
         &self.calls
     }
 
+    /// Return true once all tool calls have both a name and arguments.
     pub fn is_complete(&self) -> bool {
         !self.calls.is_empty() && self.calls.iter().all(|tc| !tc.name.is_empty() && !tc.arguments.is_empty())
     }
 
+    /// Clear all accumulated calls (starting a fresh turn).
     pub fn reset(&mut self) {
         self.calls.clear();
     }
 
+    /// Build a JSON-serialisable `Vec<Value>` of pending (non-empty-name)
+    /// tool calls, suitable for downstream inspection or replay.
     pub fn pending_args(&self) -> Vec<Value> {
         self.calls
             .iter()

src/app/runtime/stream/turn.rs

@@ -1,9 +1,14 @@
+//! Accumulates streaming LLM responses into complete message/tool-call
+//! representation via `StreamedTurn`, and provides a standalone tool-call
+//! accumulator in `tools::ToolCallAccumulator`.
 use super::StreamEvent;
 use crate::dto::chat::message::ChatMessage;
 use crate::dto::chat::tool::{ToolCall, ToolFunction};
 use serde::{Deserialize, Serialize};
 use serde_json::Value;
 
+/// Accumulates a single streaming assistant turn into its final
+/// `ChatMessage` form, including tool-call deltas and content/reasoning.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct StreamedTurn {
     pub messages: Vec<ChatMessage>,
@@ -13,6 +18,7 @@ pub struct StreamedTurn {
     pub accumulated_reasoning: String,
 }
 
+/// A single tool call being built up from streaming deltas.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct ParsedToolCall {
     pub id: String,
@@ -22,9 +28,11 @@ pub struct ParsedToolCall {
 }
 
 impl ParsedToolCall {
-    /// Attempts to parse the accumulated argument string as JSON before the tool call is
-    /// marked complete — useful for callers that want a speculative preview mid-stream.
-    /// `build_assistant_message` does its own (lossy-fallback) parse for the final message.
+    /// Attempt to parse the accumulated argument string as JSON before
+    /// the tool call is marked complete — useful for a speculative preview.
+    ///
+    /// Return: `Some(Value)` if the arguments are parsable JSON, `None`
+    /// if still partial.
     #[allow(dead_code)]
     pub fn try_parse(&self) -> Option<Value> {
         serde_json::from_str(&self.arguments).ok()
@@ -32,6 +40,7 @@ impl ParsedToolCall {
 }
 
 impl StreamedTurn {
+    /// Create an empty turn accumulator.
     pub fn new() -> Self {
         StreamedTurn {
             messages: Vec::new(),
@@ -42,6 +51,12 @@ impl StreamedTurn {
         }
     }
 
+    /// Apply a `StreamEvent` to the turn, updating accumulated content,
+    /// reasoning, and tool-call deltas.
+    ///
+    /// Flow: match on variant — `Token` appends to `accumulated_content`,
+    /// `Reasoning` to `accumulated_reasoning`, `ToolCallDelta` fills or
+    /// grows the `tool_calls` vector, `Done` sets `is_complete = true`.
     pub fn apply_event(&mut self, event: &StreamEvent) {
         match event {
             StreamEvent::Token(token) => {
@@ -84,6 +99,14 @@ impl StreamedTurn {
         }
     }
 
+    /// Finalise the turn into a `ChatMessage`, combining accumulated
+    /// reasoning (wrapped in `<think>` tags) with content and tool calls.
+    ///
+    /// Flow: if tool calls exist, build a `ChatMessage` with `tool_calls`
+    /// set; otherwise build a plain assistant message → set `content` to
+    /// the combined reasoning+content string (or `None` if empty).
+    ///
+    /// Return: a complete `ChatMessage` with role `Assistant`.
     pub fn build_assistant_message(&self) -> ChatMessage {
         let mut msg = if self.tool_calls.is_empty() {
             ChatMessage::assistant(None)

src/app/state/diff.rs

@@ -1,10 +1,16 @@
+//! Shallow state diffing — records opaque "modified" markers so the TUI
+//! knows to re-render without computing fine-grained deltas.
 use serde::{Deserialize, Serialize};
 
+/// A collection of changes tracking which parts of app state have been
+/// modified since the last render sweep.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct StateDiff {
     changes: Vec<Change>,
 }
 
+/// A single named change — currently always carries a flat `"."` path
+/// and `"modified"` kind because the system does not track granular diffs.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct Change {
     pub path: String,
@@ -12,23 +18,36 @@ pub struct Change {
 }
 
 impl StateDiff {
+    /// Create an empty diff.
     pub fn new() -> Self {
         StateDiff { changes: Vec::new() }
     }
 
+    /// Record a change at `path` of the given `kind`.
     pub fn add_change(&mut self, path: String, kind: String) {
         self.changes.push(Change { path, kind });
     }
 
+    /// Return true if no changes have been recorded.
     pub fn is_empty(&self) -> bool {
         self.changes.is_empty()
     }
 
+    /// Remove all recorded changes.
     pub fn clear(&mut self) {
         self.changes.clear();
     }
 }
 
+/// Compute a shallow diff between two serialised state values.
+///
+/// Flow: compare with `==`, return an empty vec if equal, otherwise
+/// return a single `Change { ".", "modified" }`.
+///
+/// Why: a placeholder — the current rendering model re-validates the
+/// whole viewport every frame, so fine-grained diffs are unnecessary.
+///
+/// Return: the list of changes (always 0 or 1 entry).
 pub fn compute_diff(before: &serde_json::Value, after: &serde_json::Value) -> Vec<Change> {
     if before == after {
         return Vec::new();

src/app/state/misc.rs

@@ -1,26 +1,33 @@
+//! Application-level "miscellaneous" state: scroll, input buffer,
+//! overlay stack, toasts, editor, and autocomplete.
 use std::path::PathBuf;
 use std::sync::Arc;
 use tokio::sync::RwLock;
 use super::types::Overlay;
 
+/// A shared, async-writable cache of directory entries, used to avoid
+/// re-reading a directory every render frame.
 #[derive(Clone)]
 pub struct DirCache {
     entries: Arc<RwLock<Vec<PathBuf>>>,
 }
 
 impl DirCache {
+    /// Create an empty `DirCache`.
     pub fn new() -> Self {
         DirCache {
             entries: Arc::new(RwLock::new(Vec::new())),
         }
     }
 
+    /// Replace the cached entries (async write).
     pub async fn set(&self, paths: Vec<PathBuf>) {
         let mut w = self.entries.write().await;
         *w = paths;
     }
 }
 
+/// Manages the viewport scroll offset.
 #[derive(Debug, Clone)]
 pub struct ScrollState {
     pub offset: usize,
@@ -28,6 +35,7 @@ pub struct ScrollState {
 }
 
 impl ScrollState {
+    /// Create a `ScrollState` with zero offset and 30 rows visible.
     pub fn new() -> Self {
         ScrollState {
             offset: 0,
@@ -35,19 +43,25 @@ impl ScrollState {
         }
     }
 
+    /// Scroll the viewport up by `amount` lines (increasing the offset).
+    /// Scroll the viewport up by `amount` lines (increasing the offset).
     pub fn scroll_up(&mut self, amount: usize) {
         self.offset = self.offset.saturating_add(amount);
     }
 
+    /// Scroll the viewport down by `amount` lines (decreasing the offset).
     pub fn scroll_down(&mut self, amount: usize) {
         self.offset = self.offset.saturating_sub(amount);
     }
 
+    /// Update the maximum number of visible lines.
     pub fn set_max_visible(&mut self, max: usize) {
         self.max_visible = max;
     }
 }
 
+/// The user's input buffer, cursor position, history, and autocomplete
+/// state for the chat prompt.
 #[derive(Debug, Clone)]
 pub struct InputState {
     pub buffer: String,
@@ -81,6 +95,8 @@ const COMMANDS: &[&str] = &[
 ];
 
 impl InputState {
+    /// Create an empty input state with no buffer, no history, and no
+    /// autocomplete.
     pub fn new() -> Self {
         InputState {
             buffer: String::new(),
@@ -94,6 +110,7 @@ impl InputState {
         }
     }
 
+    /// Hide the autocomplete dropdown and clear its state.
     pub fn close_autocomplete(&mut self) {
         self.autocomplete_visible = false;
         self.autocomplete_candidates.clear();
@@ -101,6 +118,12 @@ impl InputState {
         self.autocomplete_idx = 0;
     }
 
+    /// Open or refresh the autocomplete dropdown by filtering `COMMANDS`
+    /// against the current buffer prefix.
+    ///
+    /// Flow: if buffer is empty or doesn't start with `/`, close and return
+    /// → filter `COMMANDS` by prefix match → store candidates → set
+    /// `autocomplete_visible` if any candidates found.
     pub fn open_autocomplete(&mut self) {
         let trimmed = self.buffer.trim().to_string();
         if trimmed.is_empty() || !trimmed.starts_with('/') {
@@ -119,6 +142,8 @@ impl InputState {
         self.autocomplete_visible = !self.autocomplete_candidates.is_empty();
     }
 
+    /// Move the autocomplete selection up (forward=false) or down (forward=true).
+    /// Wraps around at the boundaries.
     pub fn cycle_autocomplete(&mut self, forward: bool) {
         let n = self.autocomplete_candidates.len();
         if n == 0 { return; }
@@ -129,6 +154,10 @@ impl InputState {
         }
     }
 
+    /// Accept the currently selected autocomplete candidate, placing it
+    /// in the buffer and closing the dropdown.
+    ///
+    /// Return: `true` if a candidate was selected, `false` if none existed.
     pub fn select_autocomplete(&mut self) -> bool {
         if let Some(candidate) = self.autocomplete_candidates.get(self.autocomplete_idx) {
             self.buffer = candidate.clone();
@@ -140,6 +169,8 @@ impl InputState {
         }
     }
 
+    /// Legacy inline tab-complete — opens the dropdown on first Tab press,
+    /// then cycles forward on subsequent presses.
     pub fn tab_complete(&mut self) {
         // Legacy inline tab-complete — used as a fallback when the dropdown
         // isn't visible yet. Opens the dropdown on the first Tab press.
@@ -150,23 +181,27 @@ impl InputState {
         }
     }
 
+    /// Move the cursor left by one character (if not at the start).
     pub fn char_left(&mut self) {
         if self.cursor > 0 {
             self.cursor -= 1;
         }
     }
 
+    /// Move the cursor right by one character (if not at the end).
     pub fn char_right(&mut self) {
         if self.cursor < self.buffer.len() {
             self.cursor += 1;
         }
     }
 
+    /// Insert a character at the cursor position.
     pub fn insert(&mut self, c: char) {
         self.buffer.insert(self.cursor, c);
         self.cursor += 1;
     }
 
+    /// Delete the character to the left of the cursor (backspace).
     pub fn delete_left(&mut self) {
         if self.cursor > 0 {
             self.cursor -= 1;
@@ -174,12 +209,17 @@ impl InputState {
         }
     }
 
+    /// Delete the character at the cursor position (forward delete).
     pub fn delete_right(&mut self) {
         if self.cursor < self.buffer.len() {
             self.buffer.remove(self.cursor);
         }
     }
 
+    /// Submit the current buffer: push it to history, clear the buffer,
+    /// and return the submitted text.
+    ///
+    /// Return: the text that was in the buffer before clearing.
     pub fn submit(&mut self) -> String {
         let result = self.buffer.clone();
         if !result.is_empty() {
@@ -191,6 +231,7 @@ impl InputState {
         result
     }
 
+    /// Navigate backward through input history.
     pub fn history_up(&mut self) {
         if self.history.is_empty() {
             return;
@@ -205,6 +246,7 @@ impl InputState {
         self.cursor = self.buffer.len();
     }
 
+    /// Navigate forward through input history (back toward the newest entry).
     pub fn history_down(&mut self) {
         match self.history_idx {
             Some(i) if i < self.history.len() - 1 => {
@@ -223,6 +265,8 @@ impl InputState {
     }
 }
 
+/// The "miscellaneous" slice of app state: which overlay is showing,
+/// toasts, thinking/connected flags, effort level, editor state, and tick.
 #[derive(Debug, Clone)]
 pub struct MiscState {
     pub overlay: Overlay,
@@ -237,6 +281,8 @@ pub struct MiscState {
 }
 
 impl MiscState {
+    /// Create a fresh `MiscState` with no overlay, no toasts, and default
+    /// effort level 1.
     pub fn new() -> Self {
         MiscState {
             overlay: Overlay::None,
@@ -255,6 +301,9 @@ impl MiscState {
         self.toasts.push(toast);
     }
 
+    /// Remove and return all toasts whose lifetime has expired at `now_ms`.
+    ///
+    /// Return: the expired toasts (after removal).
     pub fn drain_expired_toasts(&mut self, now_ms: i64) -> Vec<super::types::Toast> {
         let expired: Vec<_> = self.toasts.iter().filter(|t| t.expired(now_ms)).cloned().collect();
         self.toasts.retain(|t| !t.expired(now_ms));

src/app/state/mod.rs

@@ -1,3 +1,5 @@
+//! Application state: misc fields, the main `AppStateRest` struct,
+//! runtime-only state, and shared types (overlays, toasts, origins).
 pub mod misc;
 pub mod rest;
 pub mod runtime;

src/app/state/rest.rs

@@ -1,3 +1,9 @@
+//! Top-level mutable application state (`AppStateRest`) and the transcript
+//! display type it owns.
+//!
+//! `AppStateRest` is the single source-of-truth struct mutated in-place from
+//! `actions/mod.rs` and `controller/input.rs`; every other module reads it.
+
 use std::collections::VecDeque;
 use std::path::PathBuf;
 use std::sync::{Arc, Mutex};
@@ -12,6 +18,7 @@ use crate::model::app_config::AppConfig;
 use crate::model::editlog::EditLog;
 use crate::model::settings::Settings;
 
+/// A single transcript entry rendered in the TUI chat pane.
 #[derive(Debug, Clone, PartialEq)]
 pub struct ChatMessageDisplay {
     pub role: crate::dto::chat::message::Role,
@@ -20,6 +27,7 @@ pub struct ChatMessageDisplay {
 }
 
 impl ChatMessageDisplay {
+    /// Build a display entry, stamping it with the current time.
     pub fn new(role: crate::dto::chat::message::Role, content: String) -> Self {
         ChatMessageDisplay {
             role,
@@ -29,6 +37,11 @@ impl ChatMessageDisplay {
     }
 }
 
+/// The single source-of-truth state struct for the entire application.
+///
+/// Mutated in-place from two locations: `actions/mod.rs` (`apply_action`)
+/// and `controller/input.rs` (key event handlers). Read-only from every
+/// other module.
 #[derive(Clone)]
 pub struct AppStateRest {
 
@@ -58,6 +71,15 @@ pub struct AppStateRest {
 }
 
 impl AppStateRest {
+    /// Construct the initial application state for a session.
+    ///
+    /// Flow: load settings/config -> derive download/worktree dirs from
+    /// `memory_dir`'s parent -> derive `session_id` from the session dir's
+    /// file name -> build the sub-state structs.
+    ///
+    /// Why: falls back to `memory_dir` itself (with a warning) when it has
+    /// no parent, and to an empty session id when the dir name can't be
+    /// read, so construction never fails.
     pub fn new(workspace_roots: Vec<PathBuf>, session_dir: PathBuf, memory_dir: PathBuf) -> Self {
         let settings = Settings::load();
         let app_config = AppConfig::load();
@@ -105,6 +127,10 @@ impl AppStateRest {
         }
     }
 
+    /// Whether an agent turn is currently running.
+    ///
+    /// Return: `false` (and logs a warning) if the mutex is poisoned, rather
+    /// than propagating a panic.
     pub fn turn_in_flight(&self) -> bool {
         self.turn_in_flight.lock().map(|g| *g).unwrap_or_else(|_| {
             tracing::warn!("[state] turn_in_flight mutex poisoned");
@@ -114,6 +140,8 @@ impl AppStateRest {
 
 
 
+    /// Append a message to the transcript, evicting the oldest entry once
+    /// `max_lines` is exceeded, and mark both the cache and the app dirty.
     pub fn push_transcript(&mut self, msg: ChatMessageDisplay) {
         self.transcript_cache.messages.push(msg);
         if self.transcript_cache.messages.len() > self.transcript_cache.max_lines {
@@ -123,11 +151,19 @@ impl AppStateRest {
         self.dirty = true;
     }
 
+    /// Queue a toast notification for display and mark the app dirty.
     pub fn push_toast(&mut self, toast: Toast) {
         self.misc.push_toast(toast);
         self.dirty = true;
     }
 
+    /// Resolve the base directory that stores this session (grandparent of
+    /// `session_dir`, i.e. the sessions root, not the individual session
+    /// folder).
+    ///
+    /// Why: falls back progressively -- grandparent, then parent, then
+    /// `session_dir` itself -- logging a warning at each step down, so this
+    /// never fails even on a shallow path.
     pub fn store_base_dir(&self) -> std::path::PathBuf {
         self.session_dir.parent()
             .and_then(|p| p.parent())
@@ -143,10 +179,13 @@ impl AppStateRest {
             })
     }
 
+    /// Build a `ToolCtx` for tool calls originating from the main agent.
     pub fn tool_ctx(&self) -> crate::tool::ToolCtx {
         self.tool_ctx_for(Origin::Main)
     }
 
+    /// Build a `ToolCtx` scoped to the given call origin (main, subagent,
+    /// reviewer), copying workspace/session/memory paths from state.
     pub fn tool_ctx_for(&self, origin: Origin) -> crate::tool::ToolCtx {
         crate::tool::ToolCtx {
             workspaces: self.workspace_roots.clone(),

src/app/state/runtime.rs

@@ -1,6 +1,11 @@
+//! Per-session runtime state: message history, pending tool queue,
+//! background bash jobs, lesson/review counters, and the `TurnEvent`
+//! stream emitted while an agent turn is in flight.
+
 use std::path::PathBuf;
 use serde::{Deserialize, Serialize};
 
+/// Cumulative token/latency counters for a session, persisted alongside it.
 #[derive(Debug, Clone, Copy, Serialize, Deserialize, Default)]
 pub struct UsageStats {
     pub tokens_in: u64,
@@ -10,6 +15,9 @@ pub struct UsageStats {
     pub total_ms: u64,
 }
 
+/// Mutable, serializable state for one session: chat history, tool
+/// results, pending tools, background jobs, and lesson/review counters
+/// shown in the TUI status bar.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct SessionRuntime {
     pub messages: Vec<crate::dto::chat::message::ChatMessage>,
@@ -36,6 +44,7 @@ pub struct SessionRuntime {
     pub usage: UsageStats,
 }
 
+/// Record of one completed tool invocation, kept for transcript/history.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct ToolCallResult {
     pub tool_call_id: String,
@@ -45,6 +54,8 @@ pub struct ToolCallResult {
     pub duration_ms: u64,
 }
 
+/// A tool call awaiting execution, along with which execution model
+/// (inline, deferred, async) it should run under.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct PendingTool {
     pub tool_name: String,
@@ -52,6 +63,8 @@ pub struct PendingTool {
     pub execution_model: crate::app::state::types::ExecutionModel,
 }
 
+/// Reference to a background bash job tracked in session state (the actual
+/// process handle lives elsewhere; this is just the display/status record).
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct BashJobRef {
     pub id: String,
@@ -60,6 +73,8 @@ pub struct BashJobRef {
     pub running: bool,
 }
 
+/// Events emitted onto the turn-event queue while an agent turn runs,
+/// consumed by the event loop to update state and drive re-renders.
 #[derive(Debug, Clone)]
 pub enum TurnEvent {
     AssistantMessage(crate::dto::chat::message::ChatMessage),
@@ -86,6 +101,8 @@ pub enum TurnEvent {
 }
 
 impl SessionRuntime {
+    /// Create fresh runtime state for a session rooted at `session_dir`,
+    /// with all counters zeroed and `session_start` set to now.
     pub fn new(session_dir: PathBuf) -> Self {
         SessionRuntime {
             messages: Vec::new(),
@@ -113,6 +130,7 @@ impl SessionRuntime {
         }
     }
 
+    /// Append a message to the session's conversation history.
     pub fn push_message(&mut self, msg: crate::dto::chat::message::ChatMessage) {
         self.messages.push(msg);
     }

src/app/state/snapshot.rs

@@ -1,11 +1,16 @@
+//! Opaque, serializable snapshot of application state used for
+//! attach/daemon IPC transfer.
+
 use serde::{Deserialize, Serialize};
 
+/// A JSON-boxed snapshot of app state, opaque to the transport layer.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct StateSnapshot {
     pub snapshot: serde_json::Value,
 }
 
 impl StateSnapshot {
+    /// Create an empty snapshot (`{}`).
     pub fn new() -> Self {
         StateSnapshot {
             snapshot: serde_json::json!({}),
@@ -13,10 +18,16 @@ impl StateSnapshot {
     }
 }
 
+/// Serialize a snapshot to bytes for transport over the daemon socket.
+///
+/// Return: JSON-encoded bytes, or a serde error.
 pub fn serialize_snapshot(snapshot: &StateSnapshot) -> anyhow::Result<Vec<u8>> {
     Ok(serde_json::to_vec(snapshot)?)
 }
 
+/// Parse a snapshot previously produced by `serialize_snapshot`.
+///
+/// Return: the decoded `StateSnapshot`, or a serde error.
 pub fn deserialize_snapshot(data: &[u8]) -> anyhow::Result<StateSnapshot> {
     Ok(serde_json::from_slice(data)?)
 }

src/app/state/types.rs

@@ -1,6 +1,10 @@
+//! Shared small state types: toasts, overlays, the transcript cache,
+//! tool execution model, and call origin tags.
+
 use serde::{Deserialize, Serialize};
 
 
+/// Severity/category of a toast notification, used to pick its color.
 #[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)]
 pub enum ToastKind {
     Info,
@@ -10,6 +14,8 @@ pub enum ToastKind {
     Lesson,
 }
 
+/// A transient status message shown in the TUI, auto-dismissed after
+/// `lifetime_ms`.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct Toast {
     pub kind: ToastKind,
@@ -19,6 +25,7 @@ pub struct Toast {
 }
 
 impl Toast {
+    /// Create a toast with a default 5-second lifetime, stamped with now.
     pub fn new(kind: ToastKind, message: String) -> Self {
         Toast {
             kind,
@@ -28,11 +35,13 @@ impl Toast {
         }
     }
 
+    /// Whether this toast's lifetime has elapsed as of `now_ms`.
     pub fn expired(&self, now_ms: i64) -> bool {
         now_ms - self.created_at > self.lifetime_ms as i64
     }
 }
 
+/// Which modal overlay, if any, is currently shown over the main TUI view.
 #[derive(Debug, Clone, Copy, PartialEq, Eq)]
 pub enum Overlay {
     None,
@@ -56,11 +65,13 @@ pub enum Overlay {
 }
 
 impl Overlay {
+    /// Whether any overlay (i.e. anything other than `None`) is active.
     pub fn is_active(self) -> bool {
         !matches!(self, Overlay::None)
     }
 }
 
+/// Bounded ring of recent chat messages used to render the transcript view.
 #[derive(Debug, Clone, PartialEq)]
 pub struct TranscriptCache {
     pub messages: Vec<super::rest::ChatMessageDisplay>,
@@ -69,6 +80,7 @@ pub struct TranscriptCache {
 }
 
 impl TranscriptCache {
+    /// Create an empty transcript cache holding at most `max_lines` messages.
     pub fn new(max_lines: usize) -> Self {
         TranscriptCache {
             messages: Vec::new(),
@@ -78,6 +90,7 @@ impl TranscriptCache {
     }
 }
 
+/// How a pending tool call should be executed when the turn resumes.
 #[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)]
 pub enum ExecutionModel {
     Inline,
@@ -85,6 +98,8 @@ pub enum ExecutionModel {
     AsyncTokio,
 }
 
+/// Which kind of caller (main agent vs. subagent vs. reviewer) is
+/// invoking a tool, used to scope permissions and tag log/output paths.
 #[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize, Hash)]
 pub enum Origin {
     Main,
@@ -93,6 +108,7 @@ pub enum Origin {
 }
 
 impl Origin {
+    /// Short string tag for this origin, used in filenames and logs.
     pub fn tag(&self) -> String {
         match self {
             Origin::Main => "main".to_string(),

src/app/subagent/context.rs

@@ -1,8 +1,14 @@
+//! Construction of a `SubagentContext` from an `AgentDefinition`,
+//! including the default read-only tool set for reviewer agents.
+
 use std::path::PathBuf;
 use super::spawn::AgentDefinition;
 
+/// Default read-only tool names granted to `role == "reviewer"` agents.
 pub const REVIEWER_ALLOWED: &[&str] = &["read", "grep", "glob", "recall", "remember"];
 
+/// Per-invocation configuration for a subagent: prompt, allowed tools,
+/// step budget, and the session directory it should operate against.
 pub struct SubagentContext {
     pub system_prompt: String,
     pub allowed_tools: Vec<String>,
@@ -10,6 +16,14 @@ pub struct SubagentContext {
     pub session_dir: PathBuf,
 }
 
+/// Build a `SubagentContext` from an `AgentDefinition`.
+///
+/// Flow: copy optional `allowed_tools` from the def -> fall back to the
+/// reviewer-allowlist when the def has none and the role is "reviewer" ->
+/// fall back to an empty list (i.e. "all tools allowed") for other roles.
+///
+/// Return: a context with empty `system_prompt` and `session_dir`,
+/// `max_steps = 25`, and the resolved allowed-tool list.
 pub fn build_subagent_context(def: AgentDefinition) -> SubagentContext {
     let allowed_tools = def.allowed_tools.clone().unwrap_or_else(|| {
         if def.role == "reviewer" {

src/app/subagent/engine.rs

@@ -1,3 +1,7 @@
+//! Subagent execution loop: drive an LLM conversation, gate tool calls
+//! against the context's allowlist, run tools, and stream progress events
+//! to the parent via an mpsc channel.
+
 use tokio::sync::mpsc;
 use crate::dto::chat::message::ChatMessage;
 use crate::dto::provider::request::ToolDef;
@@ -5,12 +9,20 @@ use crate::tool::{all_tools, tool_defs, tool_is_risky};
 use super::context::SubagentContext;
 use super::event::SubagentEvent;
 
+/// Upper bound on agent loop steps; effectively unbounded (`usize::MAX`).
 #[allow(dead_code)]
 pub const MAX_AGENT_STEPS: usize = usize::MAX;
 
 /// Maps a subagent's allowed tool names to concrete Tool trait objects and
-/// OpenAI-style tool definitions.  When `allowed_tools` is empty every tool is
-/// available; otherwise only explicitly allowed ones are included.
+/// OpenAI-style tool definitions.
+///
+/// Flow: load `all_tools()` → if `allowed_tools` is empty, use all; else
+/// filter by membership → derive `ToolDef`s for the LLM.
+///
+/// Why: an empty allowlist means "no restriction" (matches
+/// `build_subagent_context`'s default for non-reviewer roles).
+///
+/// Return: `(tool impls, schema defs)` for the subagent to use.
 fn build_subagent_tools(allowed_tools: &[String]) -> (Vec<Box<dyn crate::tool::Tool>>, Vec<ToolDef>) {
     let all = all_tools();
     let filtered: Vec<Box<dyn crate::tool::Tool>> = if allowed_tools.is_empty() {
@@ -24,9 +36,16 @@ fn build_subagent_tools(allowed_tools: &[String]) -> (Vec<Box<dyn crate::tool::T
     (filtered, defs)
 }
 
-/// Resolves the API key, model, and base URL from the persisted application
-/// configuration rather than environment variables, matching how the main agent
-/// resolves its credentials.
+/// Resolve the API key, model, and base URL from persisted app config.
+///
+/// Flow: try the settings key for the active provider → fall back to the
+/// provider's `api_key_env` env-var → fall back to the provider's
+/// `default_api_key` → fall back to an empty string.
+///
+/// Why: matches the main agent's credential resolution exactly, so
+/// subagents automatically inherit the same provider settings.
+///
+/// Return: `(api_key, model, optional_base_url)`.
 fn resolve_provider_config() -> (String, String, Option<String>) {
     let settings = crate::model::settings::Settings::load();
     let app_config = crate::model::app_config::AppConfig::load();
@@ -54,6 +73,20 @@ fn resolve_provider_config() -> (String, String, Option<String>) {
     (api_key, model, base_url)
 }
 
+/// Synchronous subagent entry point: run up to `ctx.max_steps` iterations
+/// of the LLM tool loop.
+///
+/// Flow: inject system prompt → for each step: resolve provider config,
+/// build an LLM client, call `chat_with_tools_non_streaming`, process tool
+/// calls or collect text output → send `SubagentEvent`s on `tx` → break on
+/// first text-only (non-empty) response.
+///
+/// Why: runs synchronously on a dedicated thread so the main async event
+/// loop is not blocked. Tool gating prevents restricted or risky tools from
+/// executing unless explicitly allowed.
+///
+/// Return: the concatenated text output, or an `anyhow::Error` if the LLM
+/// call fails at any step.
 pub fn run_subagent(ctx: SubagentContext, tx: mpsc::Sender<SubagentEvent>) -> anyhow::Result<String> {
     let mut output = String::new();
     let mut messages: Vec<ChatMessage> = Vec::new();

src/app/subagent/event.rs

@@ -1,5 +1,10 @@
+//! Event variants that a running subagent can emit to its parent via the
+//! shared mpsc channel.
+
 use serde_json::Value;
 
+/// Progress and outcome events emitted by `run_subagent` as it processes
+/// LLM responses and tool calls.
 #[derive(Debug, Clone)]
 pub enum SubagentEvent {
     StepCompleted {

src/app/subagent/mod.rs

@@ -1,3 +1,6 @@
+//! Subagent management: spawning, context building, engine loop, and
+//! progress events.
+
 pub mod context;
 pub mod engine;
 pub mod event;

src/app/subagent/spawn.rs

@@ -1,5 +1,10 @@
+//! AgentDefinition -- declarative specification for instantiating a
+//! subagent from workflow scripts or programmatic calls.
+
 use serde::{Deserialize, Serialize};
 
+/// Declarative specification for instantiating a subagent: name, role,
+/// optional system prompt, allowed tools, step budget, and temperature.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct AgentDefinition {
     pub name: String,
@@ -11,6 +16,8 @@ pub struct AgentDefinition {
 }
 
 impl AgentDefinition {
+    /// Create an agent definition with the required name and role; all
+    /// optional fields start as `None`.
     pub fn new(name: String, role: String) -> Self {
         AgentDefinition {
             name,
@@ -22,6 +29,7 @@ impl AgentDefinition {
         }
     }
 
+    /// Builder method: limit this agent to at most `steps` LLM calls.
     pub fn with_max_steps(mut self, steps: usize) -> Self {
         self.max_steps = Some(steps);
         self

src/app/workflow/engine.rs

@@ -1,3 +1,7 @@
+//! Workflow engine: interprets `ScriptPrimitive` values (agent, parallel,
+//! pipeline, phase) by spawning subagents, collecting results, and
+//! managing concurrency.
+
 use std::collections::HashMap;
 use std::sync::{Arc, Mutex};
 use serde::{Deserialize, Serialize};
@@ -5,6 +9,7 @@ use super::script::{ScriptPrimitive, WorkflowScript};
 
 static FINDINGS: Mutex<Vec<String>> = Mutex::new(Vec::new());
 
+/// The lifecycle state of an agent within a workflow run.
 #[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)]
 pub enum AgentState {
     Idle,
@@ -13,6 +18,7 @@ pub enum AgentState {
     Failed,
 }
 
+/// Timestamped status of one workflow agent.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct AgentStatus {
     pub state: AgentState,
@@ -21,6 +27,7 @@ pub struct AgentStatus {
     pub error: Option<String>,
 }
 
+/// A single agent tracked within a workflow run.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct WorkflowAgent {
     pub id: String,
@@ -28,6 +35,8 @@ pub struct WorkflowAgent {
     pub status: AgentStatus,
 }
 
+/// Orchestrator for running workflow scripts: holds agent roster and a
+/// shared finding accumulator visible to all pipeline stages.
 #[derive(Debug, Clone)]
 pub struct WorkflowEngine {
     pub agents: Vec<WorkflowAgent>,
@@ -35,6 +44,7 @@ pub struct WorkflowEngine {
 }
 
 impl WorkflowEngine {
+    /// Create an empty workflow engine with no agents or findings.
     pub fn new() -> Self {
         WorkflowEngine {
             agents: Vec::new(),
@@ -43,6 +53,14 @@ impl WorkflowEngine {
     }
 }
 
+/// Spawn a single synchronous subagent with the given prompt, passing it
+/// any findings from earlier sibling agents.
+///
+/// Flow: build an `AgentDefinition` -> build a `SubagentContext` ->
+/// inject findings into the system prompt -> call `run_subagent` on a
+/// dedicated mpsc channel.
+///
+/// Return: the agent's text output, or an error on failure.
 fn spawn_single_agent(prompt: &str, findings_snapshot: Vec<String>) -> anyhow::Result<String> {
     use crate::app::subagent::context::build_subagent_context;
     use crate::app::subagent::engine::run_subagent;
@@ -74,6 +92,20 @@ fn spawn_single_agent(prompt: &str, findings_snapshot: Vec<String>) -> anyhow::R
 
 type ParallelResult = (usize, anyhow::Result<Vec<String>>);
 
+/// Recursively execute a `ScriptPrimitive` tree, respecting an overall
+/// concurrency cap for parallel branches.
+///
+/// Flow: match the primitive ->
+///   `Agent` -> `spawn_single_agent`
+///   `Parallel` -> spawn threads up to `concurrency_cap`, join
+///   `Pipeline` -> spawn threads sequentially, collect in order
+///   `Phase` -> recurse (pass-through wrapper)
+///
+/// Why: parallelism is implemented with `std::thread::spawn` and a
+/// counting semaphore so the main async event loop remains unblocked.
+///
+/// Return: a `Vec<String>` of all agent outputs (or error strings) in
+/// the order they were submitted.
 pub fn execute_primitive(
     primitive: &ScriptPrimitive,
     args: &HashMap<String, String>,
@@ -169,6 +201,14 @@ pub fn execute_primitive(
     }
 }
 
+/// Run a `WorkflowScript` with the given template arguments and produce a
+/// summary string.
+///
+/// Flow: clear the global finding store -> cap concurrency to 5 -> call
+/// `execute_primitive` on the script's root primitive -> format results
+/// into a one-line-per-agent summary.
+///
+/// Return: a human-readable summary string.
 pub fn run_workflow(script: &WorkflowScript, args: &HashMap<String, String>) -> anyhow::Result<String> {
     if let Ok(mut findings) = FINDINGS.lock() {
         findings.clear();
@@ -201,12 +241,19 @@ pub fn run_workflow(script: &WorkflowScript, args: &HashMap<String, String>) ->
     Ok(summary)
 }
 
+/// Add a finding text to the global workflow findings list, making it
+/// visible to sibling agents spawned later in the same run.
 pub fn note_finding(text: &str) {
     if let Ok(mut findings) = FINDINGS.lock() {
         findings.push(text.to_string());
     }
 }
 
+/// Simple template engine: replace `{{key}}` placeholders with values
+/// from `args`.
+///
+/// Why: a structed template engine is unnecessary for the limited
+/// use-case; this is intentionally simple and safe.
 fn resolve_template(template: &str, args: &HashMap<String, String>) -> String {
     let mut result = template.to_string();
     for (key, value) in args {
@@ -215,6 +262,9 @@ fn resolve_template(template: &str, args: &HashMap<String, String>) -> String {
     result
 }
 
+/// A counting semaphore built from a `Mutex` + `Condvar`.
+///
+/// Used by `execute_primitive` to cap concurrent parallel branches.
 struct Semaphore {
     count: Mutex<usize>,
     condvar: std::sync::Condvar,

src/app/workflow/mod.rs

@@ -1,2 +1,5 @@
+//! Workflow orchestration: a script interpreter that runs pipeline/parallel
+//! primitives across multiple subagent instances.
+
 pub mod engine;
 pub mod script;

src/app/workflow/script.rs

@@ -1,16 +1,27 @@
+//! Script primitives for the workflow engine: agent invocation, parallel
+//! execution, pipelines, and phases.
+
 use serde::{Deserialize, Serialize};
 
+/// A workflow script primitive — can be a single agent, a parallel fan-out,
+/// a sequential pipeline, or a named phase.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub enum ScriptPrimitive {
+    /// Run a single agent with the given prompt template.
     Agent(String),
+    /// Execute several primitives concurrently.
     Parallel(Vec<ScriptPrimitive>),
+    /// Execute several primitives sequentially, each waiting for the
+    /// previous to complete.
     Pipeline(Vec<ScriptPrimitive>),
+    /// A named wrapper around another primitive (used for display/tracing).
     Phase {
         name: String,
         script: Box<ScriptPrimitive>,
     },
 }
 
+/// Runtime options for a workflow execution.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct ScriptOptions {
     pub max_concurrency: usize,
@@ -28,6 +39,7 @@ impl Default for ScriptOptions {
     }
 }
 
+/// A named, versioned workflow script with its primitives and options.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct WorkflowScript {
     pub name: String,

src/controller/command.rs

@@ -1,5 +1,9 @@
+//! Slash-command parser that maps TUI `/foo` input lines into `Command`
+//! variants for the action dispatch system.
+
 use crate::app::mode::ModeKind;
 
+/// A parsed slash command from the TUI input buffer.
 #[derive(Debug, Clone, PartialEq)]
 pub enum Command {
     Help,
@@ -23,6 +27,14 @@ pub enum Command {
     Unknown(String),
 }
 
+/// Parse a slash-prefixed input line into a `Command` value.
+///
+/// Flow: trim -> check for leading `/` -> split on space (max 3 parts) ->
+/// match the first token against known commands -> extract arguments from
+/// the remaining parts.
+///
+/// Why: early return `Unknown` for non-slash lines so the caller can treat
+/// them as regular chat input.
 pub fn parse_command(text: &str) -> Command {
     let text = text.trim();
     if !text.starts_with('/') {

src/controller/input.rs

@@ -1,3 +1,7 @@
+//! Key event dispatcher: maps crossterm `KeyEvent` values into `Action`
+//! variants, with special handling for overlays, auto-complete, and the
+//! inline editor.
+
 use crossterm::event::{KeyCode, KeyEvent, KeyModifiers};
 
 use crate::app::mode;
@@ -7,6 +11,16 @@ use crate::app::state::rest::AppStateRest;
 use crate::app::state::types::Overlay;
 use crate::controller::command::parse_command;
 
+/// Translate a terminal `KeyEvent` into zero or more `Action` values
+/// based on the current application state.
+///
+/// Flow: check overlay first (Editor gets its own handler) -> match on
+/// key code and modifiers -> handle auto-complete cycles -> dispatch to
+/// `Action` variants or overlay-specific handlers.
+///
+/// Why: when Editor overlay is active, all key events are consumed by the
+/// editor handler and never reach the main action dispatch. Return `Vec`
+/// so that a single key press can trigger multiple actions.
 pub fn handle_key(key: KeyEvent, state: &mut AppStateRest) -> Vec<Action> {
     // While Editor overlay is active, route input directly to the editor handler
     if state.misc.overlay == Overlay::Editor {
@@ -192,6 +206,12 @@ pub fn handle_key(key: KeyEvent, state: &mut AppStateRest) -> Vec<Action> {
     }
 }
 
+/// Handle pressing Enter while a modal overlay is active: dispatch
+/// overlay-specific submit logic (bash, settings, todo, quit, etc.).
+///
+/// Flow: match the current overlay -> run the associated handler ->
+/// mutate state or produce actions as needed -> always return `Vec::new()`
+/// (the handler itself applies state mutations).
 fn handle_overlay_enter(state: &mut AppStateRest) -> Vec<Action> {
     match state.misc.overlay {
         Overlay::Bash => {

src/controller/mod.rs

@@ -1,2 +1,4 @@
+//! Keyboard input handling and command parsing for the TUI.
+
 pub mod command;
 pub mod input;

src/dto/chat/message.rs

@@ -1,5 +1,9 @@
+//! Chat message types shared across the DTO layer: `Role` and `ChatMessage`
+//! with convenience constructors.
+
 use serde::{Deserialize, Serialize};
 
+/// The conversation participant who authored a message.
 #[derive(Debug, Clone, PartialEq, Eq, Serialize, Deserialize)]
 pub enum Role {
     #[serde(rename = "user")]
@@ -15,6 +19,8 @@ pub enum Role {
 impl Role {
 }
 
+/// A single message in a conversation, compatible with the OpenAI/Anthropic
+/// chat-completion API structures.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct ChatMessage {
     pub role: Role,
@@ -28,6 +34,7 @@ pub struct ChatMessage {
 }
 
 impl ChatMessage {
+    /// Build a user-role message with the given text content.
     pub fn user(content: impl Into<String>) -> Self {
         ChatMessage {
             role: Role::User,
@@ -38,6 +45,7 @@ impl ChatMessage {
         }
     }
 
+    /// Build an assistant-role message with an optional text response.
     pub fn assistant(content: Option<String>) -> Self {
         ChatMessage {
             role: Role::Assistant,
@@ -48,6 +56,7 @@ impl ChatMessage {
         }
     }
 
+    /// Build a system-role message with the given instruction text.
     pub fn system(content: impl Into<String>) -> Self {
         ChatMessage {
             role: Role::System,
@@ -58,6 +67,7 @@ impl ChatMessage {
         }
     }
 
+    /// Build a tool-role result message referencing a prior tool call.
     pub fn tool_result(tool_call_id: String, content: String) -> Self {
         ChatMessage {
             role: Role::Tool,

src/dto/chat/mod.rs

@@ -1,2 +1,4 @@
+//! Chat DTO submodules: message roles/content and tool-call structures.
+
 pub mod message;
 pub mod tool;

src/dto/chat/tool.rs

@@ -1,6 +1,17 @@
+//! Tool-call DTOs embedded in assistant chat messages.
+//!
+//! Flow: provider response/stream carries `tool_calls` on an assistant
+//! message → deserialized into `ToolCall`/`ToolFunction` → harness resolves
+//! `function.name` against `all_tools()` and runs it with
+//! `sanitize_tool_arguments(function.arguments)`.
+//!
+//! Why: kept separate from `dto::provider` because tool calls are a property
+//! of a chat *message*, not of the request/response envelope.
+
 use serde::{Deserialize, Serialize};
 use serde_json::Value;
 
+/// A single tool-call request emitted by the model in an assistant message.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct ToolCall {
     pub id: String,
@@ -9,12 +20,23 @@ pub struct ToolCall {
     pub function: ToolFunction,
 }
 
+/// The function name and raw arguments payload for a `ToolCall`.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct ToolFunction {
     pub name: String,
     pub arguments: Value,
 }
 
+/// Normalize tool-call arguments into a JSON object/value.
+///
+/// Flow: some providers send `arguments` as a JSON-encoded string rather
+/// than a nested object; if `args` is a string, attempt to parse it as
+/// JSON. Objects and other value types pass through unchanged.
+///
+/// Why: falling back to the raw string on parse failure (rather than
+/// erroring) keeps the harness resilient to malformed provider output.
+///
+/// Return: the parsed `Value`, or the original `args` clone if parsing fails.
 pub fn sanitize_tool_arguments(args: &Value) -> Value {
     match args {
         Value::String(s) => {

src/dto/mod.rs

@@ -1,2 +1,5 @@
+//! Data transfer objects shared across the app: chat messages/tool calls
+//! and provider request/response/usage shapes.
+
 pub mod chat;
 pub mod provider;

src/dto/provider/mod.rs

@@ -1,3 +1,5 @@
+//! Provider-facing DTOs: chat completion request, response, and usage/cost.
+
 pub mod request;
 pub mod response;
 pub mod usage;

src/dto/provider/request.rs

@@ -1,6 +1,25 @@
+//! Outbound request DTOs for the OpenAI/Anthropic-compatible chat completions API.
+//!
+//! Flow: `harness`/`runtime` builds a `ChatRequest` from conversation state and
+//! the active tool set → serializes to JSON via `serde` → sends to the
+//! provider's `/chat/completions`-style endpoint (streaming or not).
+//!
+//! Why: fields mirror the wire format exactly (including `#[serde(rename)]`
+//! for reserved words like `type`) so no manual (de)serialization glue is
+//! needed; optional fields use `skip_serializing_if` so unset knobs are
+//! omitted rather than sent as `null`, matching provider expectations.
+
 use serde::{Deserialize, Serialize};
 use serde_json::Value;
 
+/// Outbound chat completion request body sent to an OpenAI/Anthropic-compatible provider.
+///
+/// Flow: constructed from the current message history plus optional
+/// generation knobs (temperature, max_tokens, tools, etc.) and serialized
+/// directly into the HTTP request body.
+///
+/// Return: not a function, but the value that becomes the JSON request
+/// payload for a completion call.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct ChatRequest {
     pub model: String,
@@ -21,11 +40,21 @@ pub struct ChatRequest {
     pub stream_options: Option<StreamOptions>,
 }
 
+/// Streaming options for the request; `include_usage` asks the provider to
+/// emit a final usage chunk in the SSE stream.
+///
+/// Why: usage tokens are otherwise unavailable in a streamed response since
+/// they're normally only attached to the final non-streamed completion.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct StreamOptions {
     pub include_usage: bool,
 }
 
+/// Wire format for a single tool definition sent to the provider.
+///
+/// Flow: built from the harness's registered `Tool` impls (see `all_tools()`)
+/// and attached to `ChatRequest.tools` so the model knows which functions it
+/// may call.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct ToolDef {
     #[serde(rename = "type")]
@@ -33,6 +62,10 @@ pub struct ToolDef {
     pub function: ToolFunctionDef,
 }
 
+/// Name, description, and JSON schema parameters for a tool definition.
+///
+/// Why: `parameters` is a raw `serde_json::Value` rather than a typed struct
+/// because each tool defines its own arbitrary JSON schema.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct ToolFunctionDef {
     pub name: String,

src/dto/provider/response.rs

@@ -1,5 +1,21 @@
+//! Inbound response DTOs for the non-streaming chat completions API.
+//!
+//! Flow: provider HTTP response body → `serde_json` deserializes into
+//! `ChatResponse` → caller reads `choices[0].message` for the assistant
+//! reply and `usage` for token accounting.
+//!
+//! Why: separate from the streaming SSE path (see `app/runtime/stream/mod.rs`),
+//! which parses incremental deltas rather than a single complete payload.
+
 use serde::{Deserialize, Serialize};
 
+/// Non-streaming chat completion response returned by the provider.
+///
+/// Flow: deserialized directly from the HTTP response body of a
+/// non-streaming completion call.
+///
+/// Return: not a function, but the value callers inspect for the model's
+/// reply (`choices`) and token usage (`usage`).
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct ChatResponse {
     pub id: String,
@@ -9,6 +25,10 @@ pub struct ChatResponse {
     pub created: Option<i64>,
 }
 
+/// One completion candidate within a `ChatResponse.choices` list.
+///
+/// Why: `finish_reason` is optional/string-typed since providers vary in
+/// what values they emit (e.g. `"stop"`, `"tool_calls"`, `"length"`).
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct Choice {
     pub index: u32,

src/dto/provider/usage.rs

@@ -1,5 +1,18 @@
+//! Token usage accounting DTO shared by streaming and non-streaming responses.
+//!
+//! Flow: populated from the provider's `usage` object (either the final SSE
+//! chunk when `stream_options.include_usage` is set, or the `usage` field of
+//! a non-streaming `ChatResponse`) → surfaced to the TUI for cost/token
+//! display.
+
 use serde::{Deserialize, Serialize};
 
+/// Token counts and optional cost breakdown for a single completion request.
+///
+/// Why: all fields are optional because providers differ in what they
+/// report — some omit per-token cost entirely, others omit usage altogether
+/// on certain response paths. `Default` lets callers start from an empty
+/// usage record when a provider sends none.
 #[derive(Debug, Clone, Serialize, Deserialize, Default)]
 pub struct Usage {
     pub prompt_tokens: Option<u32>,

src/ipc/client.rs

@@ -1,20 +1,37 @@
+//! Unix-socket client used by the `--attach` process to talk to a
+//! running `--daemon`.
+//!
+//! Flow: `IpcClient::connect_unix` opens a `Connection` (see `conn.rs`)
+//! to the daemon's socket path → `send`/`receive` exchange framed JSON
+//! messages (typically `ClientRequest`/`DaemonFrame` from `protocol.rs`).
+
 use anyhow::Result;
 use super::conn::Connection;
 
+/// Client-side handle for the `--attach` process: wraps a `Connection`
+/// to a daemon's Unix socket.
 pub struct IpcClient {
     conn: Connection,
 }
 
 impl IpcClient {
+    /// Connect to a daemon listening on the given Unix socket path.
+    ///
+    /// Return: `Ok(IpcClient)` on success, or an error if the socket is
+    /// missing or the daemon isn't accepting connections.
     pub fn connect_unix(path: &str) -> Result<Self> {
         let conn = Connection::connect_unix(path)?;
         Ok(IpcClient { conn })
     }
 
+    /// Serialize and send a value to the daemon (see `frame::write_frame`).
     pub fn send<T: serde::Serialize>(&mut self, value: &T) -> Result<()> {
         self.conn.send(value)
     }
 
+    /// Read and deserialize the next frame from the daemon.
+    ///
+    /// Return: `Ok(None)` if the daemon closed the connection cleanly.
     pub fn receive<T: serde::de::DeserializeOwned>(&mut self) -> Result<Option<T>> {
         self.conn.receive()
     }

src/ipc/conn.rs

@@ -1,26 +1,43 @@
+//! Framed Unix-socket connection shared by both the server (`server.rs`)
+//! and client (`client.rs`) sides of the IPC layer.
+//!
+//! Flow: `Connection` wraps a `UnixStream` (either accepted by the server
+//! or dialed by the client) → `send` serializes a value to JSON and
+//! writes it as one length-prefixed frame (`frame::write_frame`) →
+//! `receive` reads one frame and deserializes it back to the caller's
+//! type, propagating a clean peer-close as `Ok(None)`.
+
 use std::os::unix::net::UnixStream;
 use anyhow::Result;
 use super::frame;
 
+/// A framed Unix-socket connection shared by client and server sides of
+/// the IPC layer; each `send`/`receive` moves one length-prefixed JSON frame.
 pub struct Connection {
     inner: UnixStream,
 }
 
 impl Connection {
+    /// Wrap an already-connected/accepted `UnixStream`.
     pub fn from_stream(stream: UnixStream) -> Result<Self> {
         Ok(Connection { inner: stream })
     }
 
+    /// Open a new Unix-socket connection to `path`.
     pub fn connect_unix(path: &str) -> Result<Self> {
         let stream = UnixStream::connect(path)?;
         Ok(Connection { inner: stream })
     }
 
+    /// Serialize `value` to JSON and write it as one length-prefixed frame.
     pub fn send<T: serde::Serialize>(&mut self, value: &T) -> Result<()> {
         let data = frame::serialize_frame(value)?;
         frame::write_frame(&mut self.inner, &data)
     }
 
+    /// Read one length-prefixed frame and deserialize it as `T`.
+    ///
+    /// Return: `Ok(None)` on clean EOF (peer closed the connection).
     pub fn receive<T: serde::de::DeserializeOwned>(&mut self) -> Result<Option<T>> {
         let data = frame::read_frame(&mut self.inner)?;
         match data {

src/ipc/diff.rs

@@ -1,6 +1,17 @@
+//! Field-level diffing of JSON app-state snapshots, for sending only
+//! incremental changes over IPC instead of a full `StateSnapshot`.
+//!
+//! Flow: `compute_diff` recursively walks two JSON `Value`s (before/after)
+//! → for objects, recurses per key building a dotted path string; any
+//! other mismatch is recorded wholesale → results accumulate into a
+//! `StateDiff`'s `Vec<Change>`, built via `StateDiff::new`/`add_change`
+//! and reset via `clear`.
+
 use serde::{Deserialize, Serialize};
 use serde_json::Value;
 
+/// A timestamped batch of field-level changes to app state, keyed by
+/// dotted JSON path, for a given session.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct StateDiff {
     pub timestamp: i64,
@@ -8,6 +19,7 @@ pub struct StateDiff {
     pub changes: Vec<Change>,
 }
 
+/// A single field change: the JSON path and its old/new values.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct Change {
     pub path: String,
@@ -16,6 +28,7 @@ pub struct Change {
 }
 
 impl StateDiff {
+    /// Create an empty diff for `session_id`, timestamped at creation.
     pub fn new(session_id: String) -> Self {
         StateDiff {
             timestamp: chrono::Utc::now().timestamp_millis(),
@@ -24,6 +37,7 @@ impl StateDiff {
         }
     }
 
+    /// Append a single field change to the diff.
     pub fn add_change(&mut self, path: String, old_value: Option<Value>, new_value: Option<Value>) {
         self.changes.push(Change {
             path,
@@ -32,16 +46,28 @@ impl StateDiff {
         });
     }
 
+    /// Whether the diff has no recorded changes.
     pub fn is_empty(&self) -> bool {
         self.changes.is_empty()
     }
 
+    /// Drop all changes and refresh the timestamp.
     pub fn clear(&mut self) {
         self.changes.clear();
         self.timestamp = chrono::Utc::now().timestamp_millis();
     }
 }
 
+/// Recursively diff two JSON values, appending field-level `Change`s.
+///
+/// Flow: equal values short-circuit → for two objects, recurse per key
+/// (union of both maps' keys, missing side treated as `Null`) building
+/// a dotted `path` → any other value-type mismatch (or non-object diff)
+/// is recorded as one `Change` at the current `path`.
+///
+/// Why: only objects are diffed structurally; arrays and scalars are
+/// compared wholesale so a change anywhere inside them replaces the
+/// whole value rather than producing an index-level diff.
 pub fn compute_diff(before: &Value, after: &Value, path: &str, changes: &mut Vec<Change>) {
     if before == after {
         return;

src/ipc/frame.rs

@@ -1,8 +1,28 @@
+//! Length-prefixed binary framing and JSON (de)serialization helpers for
+//! the IPC wire protocol.
+//!
+//! Flow: `write_frame`/`read_frame` handle the raw byte-level framing
+//! (4-byte big-endian length header + payload) over any `Read`/`Write`;
+//! `serialize_frame`/`deserialize_frame` handle the JSON layer on top.
+//! `Connection` (see `conn.rs`) composes both layers for a full send/receive.
+//!
+//! Why: a fixed-size length prefix lets the reader know exactly how many
+//! bytes to pull before attempting to parse, avoiding partial-JSON reads
+//! over a stream socket.
+
 use std::io::{Read, Write};
 use anyhow::Result;
 
+/// Upper bound on a single frame's byte size (64 MiB), enforced on both
+/// the write and read paths to bound memory use and reject malformed or
+/// malicious oversized length headers.
 pub(crate) const MAX_FRAME_SIZE: usize = 64 * 1024 * 1024;
 
+/// Write `data` as a length-prefixed frame: 4-byte big-endian length
+/// followed by the raw bytes, then flush.
+///
+/// Why: rejects frames over `MAX_FRAME_SIZE` to bound memory use on the
+/// reading side before any bytes are read.
 pub fn write_frame<W: Write>(writer: &mut W, data: &[u8]) -> Result<()> {
     let len = data.len();
     if len > MAX_FRAME_SIZE {
@@ -15,6 +35,14 @@ pub fn write_frame<W: Write>(writer: &mut W, data: &[u8]) -> Result<()> {
     Ok(())
 }
 
+/// Read one length-prefixed frame written by `write_frame`.
+///
+/// Flow: read 4-byte length header → on clean EOF before any bytes,
+/// return `Ok(None)` (peer closed) → validate against `MAX_FRAME_SIZE`
+/// → read the payload.
+///
+/// Return: `Ok(None)` signals a graceful connection close, distinct
+/// from an `Err` mid-frame I/O failure.
 pub fn read_frame<R: Read>(reader: &mut R) -> Result<Option<Vec<u8>>> {
     let mut len_buf = [0u8; 4];
     match reader.read_exact(&mut len_buf) {
@@ -31,6 +59,7 @@ pub fn read_frame<R: Read>(reader: &mut R) -> Result<Option<Vec<u8>>> {
     Ok(Some(buf))
 }
 
+/// Serialize `value` to JSON bytes, rejecting output over `MAX_FRAME_SIZE`.
 pub fn serialize_frame<T: serde::Serialize>(value: &T) -> Result<Vec<u8>> {
     let json = serde_json::to_vec(value)?;
     if json.len() > MAX_FRAME_SIZE {
@@ -39,6 +68,7 @@ pub fn serialize_frame<T: serde::Serialize>(value: &T) -> Result<Vec<u8>> {
     Ok(json)
 }
 
+/// Deserialize a frame's raw JSON bytes into `T`.
 pub fn deserialize_frame<'a, T: serde::Deserialize<'a>>(data: &'a [u8]) -> Result<T> {
     Ok(serde_json::from_slice(data)?)
 }

src/ipc/mod.rs

@@ -1,3 +1,7 @@
+//! Unix-socket IPC layer used to connect a `--attach` TUI client to a
+//! `--daemon` process: length-prefixed framing, connection wrapper,
+//! client/server handles, and the wire protocol types.
+
 pub mod client;
 pub mod conn;
 pub mod frame;

src/ipc/protocol.rs

@@ -1,5 +1,19 @@
+//! Wire message types exchanged between an attached client and the
+//! daemon over the `Connection`/framing layer (`conn.rs`, `frame.rs`).
+//!
+//! Flow: client input events are captured as `KeyAction`/`ClientRequest`
+//! and sent to the daemon → the daemon applies them to its `AppStateRest`
+//! and replies with `DaemonFrame` variants (a flattened `StatePayload`
+//! for redraw, streamed tokens, system notes, or a close signal).
+//!
+//! Why: `StatePayload`/`MessageEntry`/`ToastEntry` are deliberately flat,
+//! serializable projections of daemon-side state so the client can
+//! redraw its TUI without sharing any in-process state with the daemon.
+
 use serde::{Deserialize, Serialize};
 
+/// Wire-serializable subset of `crossterm::event::KeyCode`, sent from
+/// an attached client to the daemon over IPC.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub enum KeyAction {
     Char(char),
@@ -19,6 +33,8 @@ pub enum KeyAction {
     Function(u8),
 }
 
+/// Messages an attached client sends to the daemon: input events, a
+/// full-line submit, terminal resize, and connection lifecycle.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub enum ClientRequest {
     Tick,
@@ -33,6 +49,7 @@ pub enum ClientRequest {
     Close,
 }
 
+/// Flattened chat message sent from daemon to client for transcript display.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct MessageEntry {
     pub role: String,
@@ -40,6 +57,7 @@ pub struct MessageEntry {
     pub timestamp: i64,
 }
 
+/// Flattened toast notification sent from daemon to client for rendering.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct ToastEntry {
     pub kind: String,
@@ -48,6 +66,8 @@ pub struct ToastEntry {
     pub lifetime_ms: u64,
 }
 
+/// Snapshot of daemon-side `AppStateRest` sent to the client after every
+/// action, enough for the client to redraw its TUI without shared state.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct StatePayload {
     pub session_id: String,
@@ -61,6 +81,7 @@ pub struct StatePayload {
     pub input_cursor: usize,
 }
 
+/// Messages the daemon sends back to an attached client.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub enum DaemonFrame {
     StateUpdate(Box<StatePayload>),

src/ipc/server.rs

@@ -1,18 +1,33 @@
+//! Unix-socket listener for the `--daemon` process.
+//!
+//! Flow: `IpcServer::bind_unix` opens/binds a Unix socket at a well-known
+//! path (clearing any stale file left by a crashed prior daemon) →
+//! `accept` blocks for the next client and wraps it as a `Connection`
+//! (see `conn.rs`) for framed request/response traffic.
+
 use std::os::unix::net::UnixListener;
 use anyhow::Result;
 use super::conn::Connection;
 
+/// Server-side handle for the `--daemon` process: listens on a Unix
+/// socket and hands out `Connection`s to accepted clients.
 pub struct IpcServer {
     listener: UnixListener,
 }
 
 impl IpcServer {
+    /// Bind a new Unix-socket listener at `path`.
+    ///
+    /// Why: removes any stale socket file at `path` first, since a prior
+    /// crashed daemon can leave one behind and `UnixListener::bind` fails
+    /// on an existing path.
     pub fn bind_unix(path: &str) -> Result<Self> {
         let _ = std::fs::remove_file(path);
         let listener = UnixListener::bind(path)?;
         Ok(IpcServer { listener })
     }
 
+    /// Block until a client connects, then wrap it as a `Connection`.
     pub fn accept(&self) -> Result<Connection> {
         let (stream, _addr) = self.listener.accept()?;
         Connection::from_stream(stream)

src/ipc/snapshot.rs

@@ -1,6 +1,17 @@
+//! Point-in-time state snapshots for external inspection/persistence of
+//! a running session (distinct from the incremental `StateDiff` in
+//! `diff.rs`).
+//!
+//! Flow: `StateSnapshot::new` builds an empty, `dirty`-marked snapshot →
+//! callers populate/replace its fields as state changes →
+//! `serialize_snapshot`/`deserialize_snapshot` move it to/from JSON bytes
+//! for storage or IPC transport.
+
 use serde::{Deserialize, Serialize};
 use serde_json::Value;
 
+/// Point-in-time summary of app state (mode, session, counts, arbitrary
+/// `payload`) used for external inspection/persistence of a running session.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct StateSnapshot {
     pub timestamp: i64,
@@ -15,6 +26,7 @@ pub struct StateSnapshot {
 }
 
 impl StateSnapshot {
+    /// Build a fresh, empty snapshot marked `dirty` for the given session.
     pub fn new(session_id: String, mode: String, model: String) -> Self {
         StateSnapshot {
             timestamp: chrono::Utc::now().timestamp_millis(),
@@ -30,11 +42,13 @@ impl StateSnapshot {
     }
 }
 
+/// Serialize a `StateSnapshot` to JSON bytes.
 pub fn serialize_snapshot(snapshot: &StateSnapshot) -> anyhow::Result<Vec<u8>> {
     let data = serde_json::to_vec(snapshot)?;
     Ok(data)
 }
 
+/// Deserialize JSON bytes back into a `StateSnapshot`.
 pub fn deserialize_snapshot(data: &[u8]) -> anyhow::Result<StateSnapshot> {
     let snapshot: StateSnapshot = serde_json::from_slice(data)?;
     Ok(snapshot)

src/main.rs

@@ -1,3 +1,10 @@
+//! Zesdex binary entry point.
+//!
+//! Parses `--daemon` / `--attach <id>` flags to select one of three
+//! process modes (single-process TUI+agent, background daemon, or
+//! attach-only TUI client), sets up file logging, and runs the
+//! corresponding event loop.
+
 use std::io;
 use std::io::Write;
 use std::sync::Mutex;
@@ -17,6 +24,16 @@ mod tool;
 mod resources;
 mod view;
 
+/// Process entry point: parse CLI flags, initialize logging, then dispatch
+/// to single-process, daemon, or attach mode.
+///
+/// Flow: parse `--daemon`/`--attach <id>` from argv → create/open the log
+/// file under the platform data dir (falling back to `/dev/null` if that
+/// fails, so a broken log path can't crash the TUI) → init tracing →
+/// reject `--daemon` + `--attach` together → dispatch.
+///
+/// Why: logging is routed to a file (never stderr/stdout) because writing
+/// to the terminal while ratatui owns the alternate screen corrupts the UI.
 fn main() -> Result<()> {
     let args: Vec<String> = std::env::args().collect();
     let is_daemon = args.iter().any(|a| a == "--daemon");
@@ -61,6 +78,17 @@ fn main() -> Result<()> {
     run_single_process()
 }
 
+/// Run zesdex as a self-contained TUI + agent loop in one process.
+///
+/// Flow: create the store, a fresh session dir, and take an exclusive
+/// session lock → build `AppStateRest` → enter raw mode / alternate
+/// screen → run the event loop → always restore the terminal (even on
+/// error) → save settings and release the session lock.
+///
+/// Why: the session lock prevents two zesdex processes from concurrently
+/// writing the same session directory. Terminal restoration happens
+/// outside `run_loop`'s `Result` so a panicking/erroring loop still
+/// leaves the user's terminal usable.
 fn run_single_process() -> Result<()> {
     let store = model::store::Store::new();
     store.ensure_dirs()?;
@@ -110,6 +138,11 @@ fn run_single_process() -> Result<()> {
     Ok(())
 }
 
+/// Map a `crossterm` key code to the wire-serializable `KeyAction`, for
+/// sending key input from an attached client to the daemon.
+///
+/// Return: `None` for key codes with no `KeyAction` equivalent (e.g.
+/// media keys), which are silently dropped.
 fn key_code_to_action(code: crossterm::event::KeyCode) -> Option<ipc::protocol::KeyAction> {
     use crossterm::event::KeyCode;
     match code {
@@ -132,6 +165,9 @@ fn key_code_to_action(code: crossterm::event::KeyCode) -> Option<ipc::protocol::
     }
 }
 
+/// Inverse of `key_code_to_action`: reconstruct a `crossterm::KeyCode`
+/// from a `KeyAction` received over IPC, for replaying it into the
+/// daemon's normal key-handling path.
 fn key_action_to_code(action: &ipc::protocol::KeyAction) -> crossterm::event::KeyCode {
     use crossterm::event::KeyCode;
     match action {
@@ -153,6 +189,15 @@ fn key_action_to_code(action: &ipc::protocol::KeyAction) -> crossterm::event::Ke
     }
 }
 
+/// Flatten the daemon's `AppStateRest` into a `StatePayload` and send it
+/// to the attached client as a `DaemonFrame::StateUpdate`.
+///
+/// Flow: map transcript messages/toasts to their wire DTOs → derive the
+/// active overlay name (or `None` if no overlay is active) → build and
+/// send one `DaemonFrame`.
+///
+/// Why: the client never shares memory with the daemon, so every action
+/// on the daemon side is followed by a full state push rather than a diff.
 fn send_daemon_update(conn: &mut ipc::conn::Connection, state: &app::state::rest::AppStateRest) -> Result<()> {
     use ipc::protocol::{DaemonFrame, MessageEntry, ToastEntry, StatePayload};
 
@@ -194,6 +239,17 @@ fn send_daemon_update(conn: &mut ipc::conn::Connection, state: &app::state::rest
     conn.send(&frame)
 }
 
+/// Apply a `StatePayload` received from the daemon onto the client's
+/// local `AppStateRest`, so the attach-mode TUI can render it.
+///
+/// Flow: copy scalar fields directly → rebuild the transcript cache from
+/// `MessageEntry`s (mapping role strings back to the `Role` enum) →
+/// resolve the overlay name string to an `Overlay` variant → rebuild
+/// toasts from `ToastEntry`s.
+///
+/// Why: unrecognized role/overlay/toast-kind strings fall back to a safe
+/// default (`Role::User`, `Overlay::None`, `ToastKind::Info`) rather than
+/// panicking, so a protocol/version mismatch degrades gracefully.
 fn apply_client_update(
     state: &mut app::state::rest::AppStateRest,
     payload: ipc::protocol::StatePayload,
@@ -260,6 +316,20 @@ fn apply_client_update(
     state.input.cursor = payload.input_cursor;
 }
 
+/// Run zesdex as a background daemon: owns the agent state, listens on a
+/// per-session Unix socket, and drives one attached client.
+///
+/// Flow: create session + lock it → bind a Unix socket under
+/// `<store>/run/<session_id>.sock` → block for a single client to
+/// `accept()` → loop reading `ClientRequest`s, translating each into
+/// `Action`(s) via the same `controller::input`/`apply_action` path the
+/// single-process mode uses, then pushing a full state update back →
+/// on `Close` or client disconnect, clean up the socket file, save
+/// settings, and release the lock.
+///
+/// Why: reuses `controller::input::handle_key` by synthesizing a
+/// `crossterm::KeyEvent` from the IPC `KeyAction`, so daemon and
+/// single-process modes share identical key-handling logic.
 fn run_daemon() -> Result<()> {
     use app::runtime::actions::{Action, apply_action};
     use ipc::protocol::ClientRequest;
@@ -362,6 +432,19 @@ fn run_daemon() -> Result<()> {
     Ok(())
 }
 
+/// Run zesdex as a TUI-only client attached to an existing daemon session.
+///
+/// Flow: connect to the daemon's Unix socket → enter raw mode/alternate
+/// screen → build a local `AppStateRest` mirror (only used for rendering
+/// and toast/overlay bookkeeping, not agent logic) → loop: poll for a
+/// terminal event (key/resize) and forward it as a `ClientRequest`, or
+/// send a `Tick` if idle → read the daemon's `DaemonFrame` reply and
+/// apply it via `apply_client_update` → redraw → exit when the daemon
+/// closes or the user quits (sending `ClientRequest::Close` first).
+///
+/// Why: Ctrl+C is intercepted locally to quit the client without going
+/// through the daemon, since the daemon has no notion of "this client
+/// wants to leave" beyond the explicit `Close` request.
 fn run_attach(session_id: &str) -> Result<()> {
     use crossterm::event::{Event, KeyCode, KeyEventKind, KeyModifiers};
     use ipc::protocol::ClientRequest;
@@ -467,6 +550,14 @@ fn run_attach(session_id: &str) -> Result<()> {
     Ok(())
 }
 
+/// Run the single-process event loop, guaranteeing terminal restoration
+/// on error.
+///
+/// Flow: delegate to `run_loop_inner` → if it errors, clear the screen
+/// and tear down raw mode / alternate screen before propagating the error.
+///
+/// Why: without this wrapper, an error inside the loop would leave the
+/// user's terminal in raw/alternate-screen mode after the process exits.
 fn run_loop(
     state: &mut app::state::rest::AppStateRest,
     terminal: &mut Terminal<CrosstermBackend<io::Stdout>>,
@@ -481,6 +572,17 @@ fn run_loop(
     result
 }
 
+/// The core single-process render/input loop.
+///
+/// Flow: until `state.quit` → drain expired toasts → draw the frame →
+/// poll for a terminal event with a 50ms timeout (keys go through
+/// `handle_key` → `apply_action`; resize and scroll map to `Action`
+/// variants directly) → always fire `Action::Tick` each iteration
+/// (drives streaming/background progress) → on exit, clear the terminal.
+///
+/// Why: the 50ms poll timeout bounds input latency while still yielding
+/// regularly for the `Tick` action, which drives async work like LLM
+/// streaming without a separate polling thread.
 fn run_loop_inner(
     state: &mut app::state::rest::AppStateRest,
     terminal: &mut Terminal<CrosstermBackend<io::Stdout>>,

src/model/agent_def/builtin.rs

@@ -1,5 +1,17 @@
+//! Hardcoded built-in subagent definitions (coder, reviewer, researcher, planner).
+
 use crate::app::subagent::spawn::AgentDefinition;
 
+/// Build the fixed list of built-in agent definitions shipped with zesdex.
+///
+/// Flow: construct each `AgentDefinition` with a name, system prompt, and
+/// allowed tool list, then collect into a `Vec`.
+///
+/// Why: these agents are always available regardless of global/session
+/// config, giving users a baseline set of roles out of the box.
+///
+/// Return: a freshly-built `Vec<AgentDefinition>` (coder, reviewer,
+/// researcher, planner).
 pub fn builtin_agents() -> Vec<AgentDefinition> {
     vec![
         AgentDefinition::new(

src/model/agent_def/global.rs

@@ -1,5 +1,19 @@
+//! Load, save, and remove user-defined agent definitions stored globally
+//! (under the store's `agents/` directory), independent of any session.
+
 use crate::app::subagent::spawn::AgentDefinition;
 
+/// Load all globally-registered agent definitions from disk.
+///
+/// Flow: resolve `<store>/agents/` → read directory → parse each `*.json`
+/// file into an `AgentDefinition`, skipping any that fail to read or parse.
+///
+/// Why: missing directory or unreadable/invalid files are silently
+/// skipped rather than failing the whole load, so one corrupt file
+/// doesn't break agent loading.
+///
+/// Return: a `Vec<AgentDefinition>`, empty if the directory doesn't exist
+/// or contains no valid definitions.
 pub fn load_global_agents() -> Vec<AgentDefinition> {
     let store = crate::model::store::Store::new();
     let agents_dir = store.base_dir.join("agents");
@@ -22,6 +36,16 @@ pub fn load_global_agents() -> Vec<AgentDefinition> {
     agents
 }
 
+/// Persist a global agent definition as `<store>/agents/<name>.json`.
+///
+/// Flow: ensure the `agents/` directory exists → serialize `def` to
+/// pretty JSON → write to a file named after `def.name`.
+///
+/// Why: writing by name overwrites any existing definition with the
+/// same name, acting as an upsert.
+///
+/// Return: `Ok(())` on success, or an error if directory creation,
+/// serialization, or the write fails.
 pub fn save_global_agent(def: &AgentDefinition) -> anyhow::Result<()> {
     let store = crate::model::store::Store::new();
     let agents_dir = store.base_dir.join("agents");
@@ -32,6 +56,14 @@ pub fn save_global_agent(def: &AgentDefinition) -> anyhow::Result<()> {
     Ok(())
 }
 
+/// Delete a global agent definition by name, if it exists.
+///
+/// Flow: resolve `<store>/agents/<name>.json` → remove the file if present.
+///
+/// Why: a no-op (not an error) when the file is already absent.
+///
+/// Return: `Ok(())` whether or not the file existed; `Err` only on an
+/// actual filesystem removal failure.
 pub fn remove_global_agent(name: &str) -> anyhow::Result<()> {
     let store = crate::model::store::Store::new();
     let path = store.base_dir.join("agents").join(format!("{}.json", name));

src/model/agent_def/mod.rs

@@ -1,3 +1,6 @@
+//! Agent definition sources: built-in defaults, global (user-wide), and
+//! per-session overrides.
+
 pub mod builtin;
 pub mod global;
 pub mod session;

src/model/agent_def/session.rs

@@ -1,6 +1,20 @@
+//! Load, save, add, and remove agent definitions scoped to a single
+//! session (`<session_dir>/agents.json`).
+
 use std::path::Path;
 use crate::app::subagent::spawn::AgentDefinition;
 
+/// Load agent definitions saved for a specific session.
+///
+/// Flow: check `<session_dir>/agents.json` exists → read → JSON-decode
+/// into `Vec<AgentDefinition>`.
+///
+/// Why: a missing file or a parse failure both degrade gracefully to an
+/// empty list (parse errors are logged via `tracing::warn!`), so a
+/// corrupt session file doesn't crash agent loading.
+///
+/// Return: the session's agent definitions, or an empty `Vec` if none
+/// exist or the file is malformed.
 pub fn load_session_agents(session_dir: &Path) -> Vec<AgentDefinition> {
     let agents_file = session_dir.join("agents.json");
     if !agents_file.exists() {
@@ -17,6 +31,13 @@ pub fn load_session_agents(session_dir: &Path) -> Vec<AgentDefinition> {
     }
 }
 
+/// Overwrite `<session_dir>/agents.json` with the given agent list.
+///
+/// Flow: serialize `agents` to pretty JSON → write to
+/// `<session_dir>/agents.json`.
+///
+/// Return: `Ok(())` on success, or an error if serialization or the
+/// write fails.
 pub fn save_session_agents(session_dir: &Path, agents: &[AgentDefinition]) -> anyhow::Result<()> {
     let agents_file = session_dir.join("agents.json");
     let content = serde_json::to_string_pretty(agents)?;
@@ -24,6 +45,14 @@ pub fn save_session_agents(session_dir: &Path, agents: &[AgentDefinition]) -> an
     Ok(())
 }
 
+/// Add or replace a session agent definition by name.
+///
+/// Flow: load existing session agents → drop any with the same name as
+/// `def` → push `def` → save the updated list.
+///
+/// Why: name-based dedup makes this an upsert rather than an append.
+///
+/// Return: `Ok(())` on success, propagating any load/save error.
 pub fn add_session_agent(session_dir: &Path, def: AgentDefinition) -> anyhow::Result<()> {
     let mut agents = load_session_agents(session_dir);
     agents.retain(|a| a.name != def.name);
@@ -31,6 +60,12 @@ pub fn add_session_agent(session_dir: &Path, def: AgentDefinition) -> anyhow::Re
     save_session_agents(session_dir, &agents)
 }
 
+/// Remove a session agent definition by name, if present.
+///
+/// Flow: load existing session agents → filter out entries matching
+/// `name` → save the updated list.
+///
+/// Return: `Ok(())` whether or not an entry with `name` existed.
 pub fn remove_session_agent(session_dir: &Path, name: &str) -> anyhow::Result<()> {
     let mut agents = load_session_agents(session_dir);
     agents.retain(|a| a.name != name);

src/model/app_config.rs

@@ -1,6 +1,11 @@
+//! Application-level configuration: LLM providers, model roles, and defaults,
+//! persisted to `app_config.json` in the store directory.
+
 use serde::{Deserialize, Serialize};
 use std::collections::HashMap;
 
+/// Top-level application config: registered providers, named model roles,
+/// and which provider/model to use by default.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct AppConfig {
     pub providers: HashMap<String, ProviderConfig>,
@@ -9,6 +14,7 @@ pub struct AppConfig {
     pub default_model: String,
 }
 
+/// Connection details for a single LLM provider (base URL, API key source).
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct ProviderConfig {
     pub api_base: String,
@@ -17,6 +23,8 @@ pub struct ProviderConfig {
     pub default_api_key: Option<String>,
 }
 
+/// A named role (e.g. "default") mapping to a specific provider/model and
+/// its generation parameters.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct ModelRole {
     pub provider: String,
@@ -57,6 +65,17 @@ impl Default for AppConfig {
 }
 
 impl AppConfig {
+    /// Load app config from disk, falling back to defaults on any failure.
+    ///
+    /// Flow: read `<store>/app_config.json` → JSON-parse → on missing file
+    /// or parse error, use `Self::default()` → merge any default providers
+    /// not already present in the loaded config.
+    ///
+    /// Why: the merge step lets newly-added default providers (e.g. a new
+    /// release adding a provider) appear even in configs saved by older
+    /// versions, without clobbering user-edited entries with the same name.
+    ///
+    /// Return: a fully-populated `AppConfig`, never fails.
     pub fn load() -> Self {
         let store = super::store::Store::new();
         let path = store.base_dir.join("app_config.json");

src/model/conversation.rs

@@ -1,5 +1,9 @@
+//! In-memory conversation state: message history plus the system prompt and
+//! model parameters used to drive the LLM.
+
 use serde::{Deserialize, Serialize};
 
+/// A single conversation's message history and generation settings.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct Conversation {
     pub messages: Vec<crate::dto::chat::message::ChatMessage>,
@@ -11,6 +15,8 @@ pub struct Conversation {
 }
 
 impl Conversation {
+    /// Create an empty conversation with the given system prompt and
+    /// session id, using default model/token/temperature settings.
     pub fn new(system_prompt: String, session_id: String) -> Self {
         Conversation {
             messages: Vec::new(),
@@ -22,10 +28,17 @@ impl Conversation {
         }
     }
 
+    /// Append a message to the conversation history.
     pub fn push(&mut self, msg: crate::dto::chat::message::ChatMessage) {
         self.messages.push(msg);
     }
 
+    /// Replace the system prompt and strip any prior `System`-role
+    /// messages from history.
+    ///
+    /// Why: the system prompt is re-injected fresh at request time via
+    /// `to_api_messages`, so stale `System` messages in `self.messages`
+    /// would be redundant/conflicting if left in place.
     pub fn rebuild_system(&mut self, new_prompt: String) {
         self.system_prompt = new_prompt;
         self.messages.retain(|m| {
@@ -33,6 +46,11 @@ impl Conversation {
         });
     }
 
+    /// Build the message list to send to the LLM API, with the system
+    /// prompt prepended.
+    ///
+    /// Return: a new `Vec` (clone of history) with a synthesized system
+    /// message at index 0.
     pub fn to_api_messages(&self) -> Vec<crate::dto::chat::message::ChatMessage> {
         let mut msgs = Vec::with_capacity(self.messages.len() + 1);
         msgs.push(crate::dto::chat::message::ChatMessage::system(&self.system_prompt));
@@ -40,6 +58,8 @@ impl Conversation {
         msgs
     }
 
+    /// Number of messages in the conversation history (excluding the
+    /// synthesized system message).
     pub fn len(&self) -> usize {
         self.messages.len()
     }

src/model/editlog.rs

@@ -1,5 +1,10 @@
+//! Append-only JSONL edit log recording every file mutation made by tools,
+//! for audit and undo/history purposes.
+
 use serde::{Deserialize, Serialize};
 
+/// A single recorded file edit: which tool made it, to which path, why,
+/// and a content hash/size delta for verification.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct EditLogEntry {
     pub ts: i64,
@@ -12,6 +17,7 @@ pub struct EditLogEntry {
     pub session_id: String,
 }
 
+/// In-memory view of a session's edit log, backed by `edits.jsonl` on disk.
 #[derive(Debug, Clone)]
 pub struct EditLog {
     pub entries: Vec<EditLogEntry>,
@@ -19,6 +25,8 @@ pub struct EditLog {
 }
 
 impl EditLog {
+    /// Open (or start tracking) the edit log for a session directory,
+    /// replaying any existing `edits.jsonl` into memory.
     pub fn new(session_dir: &std::path::Path) -> Self {
         let path = session_dir.join("edits.jsonl");
         let entries = Self::load_from_disk(&path);
@@ -40,6 +48,17 @@ impl EditLog {
             .collect()
     }
 
+    /// Append one entry to `edits.jsonl` on disk and to the in-memory log.
+    ///
+    /// Flow: serialize `entry` to a JSON line → ensure parent dir exists →
+    /// open the file in append mode → write the line → push into
+    /// `self.entries`.
+    ///
+    /// Why: appending (not rewriting) keeps the log durable and cheap even
+    /// as it grows across a long session.
+    ///
+    /// Return: `Ok(())` on success; an `io::Error` if serialization or
+    /// any filesystem operation fails.
     pub fn append(&mut self, entry: EditLogEntry) -> std::io::Result<()> {
         let line = serde_json::to_string(&entry)? + "\n";
         let parent = self.path.parent().unwrap();
@@ -54,6 +73,7 @@ impl EditLog {
         Ok(())
     }
 
+    /// Number of edit entries recorded so far in this log.
     pub fn len(&self) -> usize {
         self.entries.len()
     }

src/model/memory.rs

@@ -1,6 +1,11 @@
+//! Long-term agent memory: markdown files with YAML-ish frontmatter storing
+//! lessons/references, plus slugified filenames and export/import helpers.
+
 use std::path::{Path, PathBuf};
 use serde::{Deserialize, Serialize};
 
+/// A single memory entry (lesson, reference, etc.) with frontmatter
+/// metadata and free-form markdown content.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct Memory {
     pub name: String,
@@ -18,6 +23,17 @@ pub struct Memory {
 }
 
 impl Memory {
+    /// Convert an arbitrary string into a filesystem-safe slug.
+    ///
+    /// Flow: lowercase → replace non-alphanumeric chars with `-` →
+    /// collapse/trim repeated `-` by splitting on it and rejoining
+    /// non-empty parts.
+    ///
+    /// Why: rejects empty or overly long (>80 char) results so callers
+    /// don't write memories with degenerate or unwieldy filenames.
+    ///
+    /// Return: `Some(slug)` on success, `None` if the input slugifies to
+    /// empty or exceeds 80 characters.
     pub fn slugify(s: &str) -> Option<String> {
         let slug: String = s
             .to_lowercase()
@@ -35,11 +51,27 @@ impl Memory {
         Some(slug)
     }
 
+    /// Compute the on-disk path for a memory of the given name.
+    ///
+    /// Why: falls back to a fixed `"memory"` slug when `name` slugifies
+    /// to nothing, so a path is always produced.
     pub fn path(memory_dir: &Path, name: &str) -> PathBuf {
         let slug = Self::slugify(name).unwrap_or_else(|| "memory".to_string());
         slug_path(memory_dir, &format!("{}.md", slug))
     }
 
+    /// Serialize this memory to markdown-with-frontmatter and write it
+    /// atomically to disk.
+    ///
+    /// Flow: build the frontmatter block (name/description/kind/timestamps/
+    /// lifecycle/optional fields) → concatenate with body content → write
+    /// to a temp file → rename into place.
+    ///
+    /// Why: write-then-rename avoids leaving a half-written memory file if
+    /// the process is interrupted mid-write.
+    ///
+    /// Return: `Ok(())` on success, or an `io::Error` from directory
+    /// creation, the temp write, or the rename.
     pub fn write(&self, memory_dir: &Path) -> std::io::Result<()> {
         let path = Self::path(memory_dir, &self.name);
         let parent = path.parent().unwrap();
@@ -65,12 +97,29 @@ impl Memory {
         Ok(())
     }
 
+    /// Read and parse a memory file by name.
+    ///
+    /// Return: the parsed `Memory`, or an `io::Error` if the file is
+    /// missing or its frontmatter is malformed (see `parse`).
     pub fn read(memory_dir: &Path, name: &str) -> std::io::Result<Self> {
         let path = Self::path(memory_dir, name);
         let content = std::fs::read_to_string(&path)?;
         Self::parse(&content)
     }
 
+    /// Parse a memory file's contents (frontmatter + body) into a `Memory`.
+    ///
+    /// Flow: strip leading `---\n` → split on the first `\n---\n` into
+    /// frontmatter and body → parse frontmatter lines as `key: value`
+    /// pairs into a map → build `Memory` fields from the map with
+    /// sensible defaults for missing keys.
+    ///
+    /// Why: unknown/missing frontmatter keys degrade to defaults (e.g.
+    /// `kind` → "reference", `lifecycle` → "new") rather than failing,
+    /// so older or hand-edited memory files still parse.
+    ///
+    /// Return: `Err(InvalidData)` only if the `---` frontmatter delimiter
+    /// itself is missing; otherwise `Ok(Memory)`.
     pub fn parse(content: &str) -> std::io::Result<Self> {
         let content = content.strip_prefix("---\n").unwrap_or(content);
         let parts: Vec<&str> = content.splitn(2, "\n---\n").collect();
@@ -103,6 +152,9 @@ impl Memory {
         })
     }
 
+    /// Delete a memory file by name, if it exists.
+    ///
+    /// Return: `Ok(())` whether or not the file existed.
     pub fn remove(memory_dir: &Path, name: &str) -> std::io::Result<()> {
         let path = Self::path(memory_dir, name);
         if path.exists() {
@@ -111,6 +163,13 @@ impl Memory {
         Ok(())
     }
 
+    /// List the slugs of all memory files in a directory.
+    ///
+    /// Flow: read the directory → keep entries ending in `.md` → exclude
+    /// the special `MEMORY.md` summary file → strip the `.md` suffix.
+    ///
+    /// Return: slugs (without extension); empty `Vec` if the directory
+    /// can't be read.
     pub fn list(memory_dir: &Path) -> Vec<String> {
         let entries = match std::fs::read_dir(memory_dir) {
             Ok(e) => e,
@@ -129,6 +188,14 @@ impl Memory {
     }
 }
 
+/// Sanitize a raw filename into a safe path under `memory_dir`.
+///
+/// Flow: replace any char that isn't alphanumeric, `.`, or `-` with `-` →
+/// strip leading dots (prevents dotfiles / path traversal via `..`) →
+/// join to `memory_dir`, falling back to `"memory.md"` if empty.
+///
+/// Why: leading-dot stripping specifically blocks accidental hidden
+/// files and `..`-style traversal attempts embedded in `raw`.
 pub fn slug_path(memory_dir: &Path, raw: &str) -> PathBuf {
     let clean: String = raw.chars()
         .map(|c| if c.is_ascii_alphanumeric() || c == '.' || c == '-' { c } else { '-' })
@@ -137,6 +204,14 @@ pub fn slug_path(memory_dir: &Path, raw: &str) -> PathBuf {
     memory_dir.join(if clean.is_empty() { "memory.md" } else { &clean })
 }
 
+/// Export all memories in `memory_dir` to a single JSON file.
+///
+/// Flow: list memory slugs → read+parse each into a `Memory` (skipping
+/// any that fail) → serialize the collected `Vec<Memory>` to pretty JSON
+/// → write to `output`.
+///
+/// Return: `Ok(())` on success, or an `io::Error` from serialization or
+/// the write.
 pub fn export_lessons(memory_dir: &Path, output: &Path) -> std::io::Result<()> {
     let names = Memory::list(memory_dir);
     let lessons: Vec<Memory> = names.iter()
@@ -147,6 +222,17 @@ pub fn export_lessons(memory_dir: &Path, output: &Path) -> std::io::Result<()> {
     std::fs::write(output, data)?;
     Ok(())
 }
+/// Import memories from a JSON export file into `memory_dir`, skipping
+/// duplicates.
+///
+/// Flow: read+JSON-decode `input` into `Vec<Memory>` → build a set of
+/// existing slugs in `memory_dir` → for each lesson not already present
+/// (by slug), write it to disk and count it.
+///
+/// Why: slug-based dedup makes repeated imports idempotent — re-running
+/// import on the same file won't overwrite or duplicate existing memories.
+///
+/// Return: the number of memories actually imported (skips existing ones).
 pub fn import_lessons(memory_dir: &Path, input: &Path) -> std::io::Result<usize> {
     let data = std::fs::read_to_string(input)?;
     let lessons: Vec<Memory> = serde_json::from_str(&data)

src/model/mod.rs

@@ -1,3 +1,6 @@
+//! Persistence and domain model layer: sessions, conversations, memory,
+//! message log (SQLite), edit log, and app/settings config.
+
 pub mod app_config;
 pub mod editlog;
 pub mod memory;

src/model/msglog/blobs.rs

@@ -1,6 +1,15 @@
+//! Binary blob storage in the message-log SQLite database (e.g. images,
+//! attachments), keyed by session id and an arbitrary blob key.
+
 use rusqlite::{Connection, params};
 use anyhow::Result;
 
+/// Insert or overwrite a blob for a session under `blob_key`.
+///
+/// Flow: compute current timestamp → `INSERT OR REPLACE` into `blobs`
+/// keyed on `(session_id, blob_key)`.
+///
+/// Return: `Ok(())` on success, or the underlying SQLite error.
 pub fn store_blob(conn: &Connection, session_id: &str, blob_key: &str, data: &[u8], mime_type: Option<&str>) -> Result<()> {
     let created_at = chrono::Utc::now().timestamp_millis();
     conn.execute(
@@ -10,6 +19,10 @@ pub fn store_blob(conn: &Connection, session_id: &str, blob_key: &str, data: &[u
     Ok(())
 }
 
+/// Fetch a blob's bytes for a session by key.
+///
+/// Return: `Ok(Some(data))` if found, `Ok(None)` if no matching row
+/// exists, `Err` for any other SQLite failure.
 pub fn retrieve_blob(conn: &Connection, session_id: &str, blob_key: &str) -> Result<Option<Vec<u8>>> {
     let result = conn.query_row(
         "SELECT data FROM blobs WHERE session_id = ?1 AND blob_key = ?2",
@@ -23,6 +36,10 @@ pub fn retrieve_blob(conn: &Connection, session_id: &str, blob_key: &str) -> Res
     }
 }
 
+/// Delete a blob for a session by key.
+///
+/// Return: `Ok(true)` if a row was deleted, `Ok(false)` if no matching
+/// row existed.
 #[allow(dead_code)]
 pub fn delete_blob(conn: &Connection, session_id: &str, blob_key: &str) -> Result<bool> {
     let rows = conn.execute(
@@ -32,6 +49,10 @@ pub fn delete_blob(conn: &Connection, session_id: &str, blob_key: &str) -> Resul
     Ok(rows > 0)
 }
 
+/// List all blob keys stored for a session, oldest first.
+///
+/// Return: `Ok(Vec<String>)` of keys ordered by `created_at`, or the
+/// underlying SQLite error.
 pub fn list_blob_keys(conn: &Connection, session_id: &str) -> Result<Vec<String>> {
     let mut stmt = conn.prepare(
         "SELECT blob_key FROM blobs WHERE session_id = ?1 ORDER BY created_at ASC"

src/model/msglog/mod.rs

@@ -1,3 +1,6 @@
+//! SQLite-backed message log: per-session `messages.sqlite` storing chat
+//! messages, blobs, and archive/summary metadata.
+
 pub mod blobs;
 pub mod query;
 pub mod schema;
@@ -5,6 +8,14 @@ pub mod schema;
 pub use blobs::store_blob;
 pub use query::insert_message;
 
+/// Open (creating if needed) a session's `messages.sqlite` and ensure its
+/// schema is initialized.
+///
+/// Flow: resolve `<session_dir>/messages.sqlite` → create parent dirs →
+/// open a SQLite connection → run `schema::init_schema`.
+///
+/// Return: an open, schema-ready `Connection`, or an error if any step
+/// fails.
 pub fn open_or_create(session_dir: &std::path::Path) -> anyhow::Result<rusqlite::Connection> {
     let path = session_dir.join("messages.sqlite");
     if let Some(parent) = path.parent() {

src/model/msglog/query.rs

@@ -1,7 +1,16 @@
+//! Insert queries against the message log's `messages` table.
+
 use rusqlite::{Connection, params};
 use anyhow::Result;
 use crate::dto::chat::message::{ChatMessage, Role};
 
+/// Insert a chat message into the session's message log.
+///
+/// Flow: extract optional content/tool_call_id/tool_name → serialize
+/// `tool_calls` to a JSON string if present → map `Role` to its string
+/// column value → `INSERT` the row with the current timestamp.
+///
+/// Return: the new row's `rowid` on success, or the underlying error.
 pub fn insert_message(conn: &Connection, session_id: &str, msg: &ChatMessage) -> Result<i64> {
     let content = msg.content.as_deref();
     let tool_call_id = msg.tool_call_id.as_deref();

src/model/msglog/schema.rs

@@ -1,6 +1,15 @@
+//! SQLite schema definition for the message log database.
+
 use rusqlite::Connection;
 use anyhow::Result;
 
+/// Create the message log's tables and indexes if they don't already
+/// exist (`messages`, `archives`, `blobs`).
+///
+/// Why: idempotent via `CREATE TABLE/INDEX IF NOT EXISTS`, so it's safe
+/// to call on every `open_or_create`.
+///
+/// Return: `Ok(())` on success, or the underlying SQLite error.
 pub fn init_schema(conn: &Connection) -> Result<()> {
     conn.execute_batch(
         "

src/model/msglog/summary.rs

@@ -1,5 +1,9 @@
+//! Session archive/summary metadata tracked alongside the message log
+//! (title, model, counts, and a rolling text summary).
+
 use serde::{Deserialize, Serialize};
 
+/// Summary metadata for one archived/summarized session.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct SummaryRecord {
     pub session_id: String,
@@ -13,6 +17,8 @@ pub struct SummaryRecord {
 }
 
 impl SummaryRecord {
+    /// Create a fresh summary record with zeroed counts and an empty
+    /// summary, timestamped to now.
     pub fn new(session_id: String, title: String, model: String) -> Self {
         let now = chrono::Utc::now().timestamp_millis();
         SummaryRecord {
@@ -27,11 +33,13 @@ impl SummaryRecord {
         }
     }
 
+    /// Replace the summary text and bump `updated_at`.
     pub fn update_summary(&mut self, summary: String) {
         self.summary = summary;
         self.updated_at = chrono::Utc::now().timestamp_millis();
     }
 
+    /// Add to the running message/token counts and bump `updated_at`.
     pub fn increment_counts(&mut self, messages: usize, tokens: usize) {
         self.message_count += messages;
         self.token_count += tokens;

src/model/session.rs

@@ -1,7 +1,12 @@
+//! Session metadata: id, title, workspace roots, and message/token counts,
+//! persisted as `session.json` per session directory.
+
 use std::path::{Path, PathBuf};
 use serde::{Deserialize, Serialize};
 use chrono::Utc;
 
+/// Metadata for one conversation session (distinct from the message
+/// history itself, which lives in `Conversation`/the msglog).
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct Session {
     pub id: String,
@@ -17,6 +22,8 @@ pub struct Session {
 }
 
 impl Session {
+    /// Create a new session with the given id/title, defaulting the
+    /// model, workspace root (current dir), and counters.
     pub fn new(id: String, title: String) -> Self {
         let now = Utc::now().timestamp_millis();
         Session {
@@ -33,14 +40,25 @@ impl Session {
         }
     }
 
+    /// Compute this session's directory under `<base_dir>/sessions/<id>`.
     pub fn session_dir(&self, base_dir: &Path) -> PathBuf {
         base_dir.join("sessions").join(&self.id)
     }
 
+    /// Compute this session's `conversation.json` path.
     pub fn conversation_path(&self, base_dir: &Path) -> PathBuf {
         self.session_dir(base_dir).join("conversation.json")
     }
 
+    /// Persist this session's metadata to `session.json`, atomically.
+    ///
+    /// Flow: ensure the session directory exists → serialize to pretty
+    /// JSON → write to `session.json.tmp` → rename over `session.json`.
+    ///
+    /// Why: write-then-rename avoids a torn/partial `session.json` if
+    /// interrupted mid-write.
+    ///
+    /// Return: `Ok(())` on success, or an `io::Error` from any step.
     pub fn save(&self, base_dir: &Path) -> std::io::Result<()> {
         let dir = self.session_dir(base_dir);
         std::fs::create_dir_all(&dir)?;
@@ -52,6 +70,10 @@ impl Session {
         Ok(())
     }
 
+    /// Load a session's metadata by id from `<base_dir>/sessions/<id>/session.json`.
+    ///
+    /// Return: the parsed `Session`, or an `io::Error` if the file is
+    /// missing or malformed.
     pub fn load(id: &str, base_dir: &Path) -> std::io::Result<Self> {
         let path = base_dir.join("sessions").join(id).join("session.json");
         let data = std::fs::read_to_string(path)?;
@@ -59,6 +81,14 @@ impl Session {
         Ok(session)
     }
 
+    /// List all loadable sessions under `<base_dir>/sessions/`.
+    ///
+    /// Flow: read the sessions directory → keep subdirectories → attempt
+    /// `Session::load` for each by its directory name, discarding any
+    /// that fail to load.
+    ///
+    /// Return: a `Vec<Session>`, empty if the directory can't be read or
+    /// contains no valid sessions.
     pub fn list(base_dir: &Path) -> Vec<Self> {
         let sessions_dir = base_dir.join("sessions");
         let entries = match std::fs::read_dir(&sessions_dir) {

src/model/session_lock.rs

@@ -1,12 +1,19 @@
+//! PID-file based advisory lock preventing two processes from operating on
+//! the same session directory concurrently.
+
 use std::path::{Path, PathBuf};
 use std::fs;
 
+/// A PID-file lock (`<session_dir>/.lock`) tied to the current process,
+/// auto-removed on drop.
 pub struct SessionLock {
     path: PathBuf,
     pid: u32,
 }
 
 impl SessionLock {
+    /// Construct a lock handle for a session directory (does not acquire
+    /// the lock yet — call `try_lock`).
     pub fn new(session_dir: &Path) -> Self {
         SessionLock {
             path: session_dir.join(".lock"),
@@ -14,6 +21,19 @@ impl SessionLock {
         }
     }
 
+    /// Attempt to acquire the session lock.
+    ///
+    /// Flow: if `.lock` exists, read the PID inside it and check
+    /// `is_alive` — if that process is still running, fail to acquire →
+    /// otherwise (no lock file, unreadable PID, or dead owner) write our
+    /// own PID into `.lock` and succeed.
+    ///
+    /// Why: a stale lock file from a crashed process must not permanently
+    /// block new sessions, so liveness is re-checked via `kill(pid, 0)`
+    /// rather than trusting the file's mere existence.
+    ///
+    /// Return: `Ok(true)` if acquired, `Ok(false)` if another live
+    /// process holds it, `Err` on I/O failure.
     pub fn try_lock(&self) -> std::io::Result<bool> {
         if self.path.exists() {
             let content = fs::read_to_string(&self.path).unwrap_or_default();
@@ -27,10 +47,12 @@ impl SessionLock {
         Ok(true)
     }
 
+    /// Explicitly release the lock by removing the lock file.
     pub fn unlock(&self) {
         let _ = fs::remove_file(&self.path);
     }
 
+    /// Check whether a process with the given PID is currently alive.
     fn is_alive(&self, pid: u32) -> bool {
         // SAFETY: `libc::kill(pid, 0)` does not send a signal; it only checks
         // whether the process exists and the caller has permission to signal
@@ -40,6 +62,8 @@ impl SessionLock {
 }
 
 impl Drop for SessionLock {
+    /// Release the lock automatically when the guard goes out of scope,
+    /// so an ungracefully-exited process doesn't leave a dangling lock.
     fn drop(&mut self) {
         let _ = fs::remove_file(&self.path);
     }

src/model/settings.rs

@@ -1,5 +1,15 @@
+//! User-configurable settings persisted as JSON in the store's base directory.
+//!
+//! `Settings::load` / `Settings::save` are the only entry points; every field
+//! falls back to a hardcoded default via `Default for Settings` when the file
+//! is missing or fails to parse.
+
 use serde::{Deserialize, Serialize};
 
+/// Controls how much network access the agent is permitted during a session.
+///
+/// `Off` disables outbound requests entirely, `ReadOnly` allows fetches but
+/// no mutating calls, `Full` permits everything. Defaults to `Off`.
 #[derive(Debug, Clone, PartialEq, Eq, Serialize, Deserialize)]
 #[derive(Default)]
 pub enum InternetMode {
@@ -11,6 +21,10 @@ pub enum InternetMode {
 
 
 
+/// Top-level application settings, serialized to `settings.json` in the store dir.
+///
+/// Why: a single flat struct rather than nested config so the JSON file stays
+/// human-editable; unknown/missing fields on load fall back to `Default`.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct Settings {
     pub internet_mode: InternetMode,
@@ -49,6 +63,12 @@ impl Default for Settings {
 }
 
 impl Settings {
+    /// Load settings from `<store_base_dir>/settings.json`.
+    ///
+    /// Flow: read file → parse JSON → fall back to `Settings::default()` on
+    /// any failure (missing file, unreadable, malformed JSON).
+    ///
+    /// Return: always succeeds; never surfaces I/O or parse errors to the caller.
     pub fn load() -> Self {
         let store = super::store::Store::new();
         let path = store.base_dir.join("settings.json");
@@ -58,6 +78,11 @@ impl Settings {
             .unwrap_or_default()
     }
 
+    /// Serialize and write settings to `<store_base_dir>/settings.json`.
+    ///
+    /// Flow: ensure base dir exists → pretty-print JSON → write to disk.
+    ///
+    /// Return: `Err` if the directory can't be created or the write fails.
     pub fn save(&self) -> std::io::Result<()> {
         let store = super::store::Store::new();
         std::fs::create_dir_all(&store.base_dir)?;

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)?;

src/resources.rs

@@ -1,3 +1,6 @@
+//! Compile-time embedded text resources: the system prompt, tool descriptions,
+//! and the in-app help screen shown on Ctrl+H.
+
 pub const SYSTEM_PROMPT: &str = include_str!("../src-misc/system-prompt.txt");
 pub const SYSTEM_TOOLS: &str = include_str!("../src-misc/system-tools.txt");
 

src/service/mod.rs

@@ -1,2 +1,4 @@
+//! External service integrations: the LLM provider HTTP client and OAuth flows.
+
 pub mod provider;
 pub mod oauth;

src/service/oauth/loopback.rs

@@ -1,28 +1,46 @@
+//! Minimal loopback HTTP server for capturing OAuth authorization-code redirects.
+
 use std::io::{Read, Write};
 use std::net::{TcpListener, TcpStream};
 
+/// A single-use HTTP listener on `127.0.0.1` that receives the OAuth
+/// `?code=...` redirect and serves back a static confirmation page.
 pub struct LoopbackServer {
     listener: TcpListener,
     port: u16,
 }
 
 impl LoopbackServer {
+    /// Bind to an OS-assigned free port on localhost.
+    ///
+    /// Return: `Err` if the loopback interface can't be bound.
     pub fn bind() -> std::io::Result<Self> {
         let listener = TcpListener::bind("127.0.0.1:0")?;
         let port = listener.local_addr()?.port();
         Ok(LoopbackServer { listener, port })
     }
 
+    /// The redirect URI to hand to the OAuth authorization endpoint.
     pub fn redirect_uri(&self) -> String {
         format!("http://127.0.0.1:{}/callback", self.port)
     }
 
+    /// Block until one HTTP request arrives, then extract its `code` query param.
+    ///
+    /// Flow: accept one connection → apply read timeout → parse request line
+    /// → respond 200/400 depending on whether a code was found.
+    ///
+    /// Return: `Err(InvalidData)` if no `code` param is present in the request.
     pub fn wait_for_code(&self, timeout_ms: u64) -> std::io::Result<String> {
         let (mut stream, _) = self.listener.accept()?;
         stream.set_read_timeout(Some(std::time::Duration::from_millis(timeout_ms)))?;
         Self::read_callback(&mut stream)
     }
 
+    /// Read and parse a single HTTP callback request off `stream`, replying with a status page.
+    ///
+    /// Why: writes the HTTP response before returning so the browser tab
+    /// shows a result regardless of whether the code was found.
     fn read_callback(stream: &mut TcpStream) -> std::io::Result<String> {
         let mut buf = [0u8; 4096];
         let n = stream.read(&mut buf)?;
@@ -38,6 +56,9 @@ impl LoopbackServer {
         code.ok_or_else(|| std::io::Error::new(std::io::ErrorKind::InvalidData, "code not found in callback"))
     }
 
+    /// Extract and percent-decode the `code` query parameter from an HTTP request line.
+    ///
+    /// Return: `None` if the request is malformed or has no `code` param.
     fn extract_code(request: &str) -> Option<String> {
         let line = request.lines().next()?;
         let path = line.split(' ').nth(1)?;
@@ -52,6 +73,11 @@ impl LoopbackServer {
     }
 }
 
+/// Percent-decode a string (e.g. `%20` -> space).
+///
+/// Why: invalid escape sequences (missing/non-hex digits) are passed through
+/// literally as `%` rather than erroring, since this only handles a redirect
+/// query param, not untrusted binary data.
 fn urlencoding(s: &str) -> String {
     let mut result = String::with_capacity(s.len());
     let mut chars = s.chars();

src/service/oauth/manager.rs

@@ -1,6 +1,9 @@
+//! OAuth 2.0 authorization-code + PKCE flow: token exchange and authorization URL building.
+
 use std::time::{SystemTime, UNIX_EPOCH};
 use serde::{Deserialize, Serialize};
 
+/// An OAuth access token plus its refresh token and absolute expiry (unix seconds).
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct OAuthToken {
     pub access_token: String,
@@ -12,6 +15,7 @@ pub struct OAuthToken {
 impl OAuthToken {
 }
 
+/// Static configuration for an OAuth provider: endpoints, client identity, and requested scopes.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct OAuthConfig {
     pub auth_url: String,
@@ -33,6 +37,7 @@ impl Default for OAuthConfig {
     }
 }
 
+/// Drives one OAuth flow: holds config, the current token (if any), and an HTTP client.
 pub struct OAuthManager {
     pub config: OAuthConfig,
     pub token: Option<OAuthToken>,
@@ -40,6 +45,7 @@ pub struct OAuthManager {
 }
 
 impl OAuthManager {
+    /// Create a manager for the given provider config with no token yet acquired.
     pub fn new(config: OAuthConfig) -> Self {
         OAuthManager {
             config,
@@ -48,6 +54,12 @@ impl OAuthManager {
         }
     }
 
+    /// Exchange an authorization code for an access token via the provider's token endpoint.
+    ///
+    /// Flow: POST form-encoded grant to `token_url` → parse JSON body →
+    /// compute absolute `expires_at` from `expires_in` → store on `self.token`.
+    ///
+    /// Return: `Err(String)` on network failure, non-2xx status, or a missing `access_token` field.
     pub fn exchange_code(&mut self, code: &str, redirect_uri: &str, code_verifier: &str) -> Result<(), String> {
         let mut params = std::collections::HashMap::new();
         params.insert("grant_type", "authorization_code");
@@ -83,13 +95,17 @@ impl OAuthManager {
         Ok(())
     }
 
+    /// Build the provider's authorization URL with PKCE and state params attached.
+    ///
+    /// Why: refuses to build a URL if `auth_url` is missing or invalid. Previously
+    /// this silently fell back to https://example.com, which produced a valid-looking
+    /// auth URL pointing at the wrong server and leaked client credentials in
+    /// query params. Returning an empty string signals failure to callers, who
+    /// can prompt the user to fix the OAuth config instead of starting a flow
+    /// against a wrong host.
+    ///
+    /// Return: the full authorization URL, or `""` if `auth_url` is empty/unparseable.
     pub fn build_auth_url(&self, redirect_uri: &str, state: &str, code_challenge: &str) -> String {
-        // Refuse to build a URL if `auth_url` is missing or invalid. Previously this
-        // silently fell back to https://example.com, which produced a valid-looking
-        // auth URL pointing at the wrong server and leaked client credentials in
-        // query params. Returning an empty string signals failure to callers, who
-        // can prompt the user to fix the OAuth config instead of starting a flow
-        // against a wrong host.
         let mut url = match url::Url::parse(&self.config.auth_url) {
             Ok(u) if !self.config.auth_url.is_empty() => u,
             _ => {

src/service/oauth/mod.rs

@@ -1,3 +1,6 @@
+//! OAuth 2.0 authorization-code + PKCE support: verifier/challenge generation,
+//! the loopback redirect server, and the token-exchange manager.
+
 pub mod pkce;
 pub mod loopback;
 pub mod manager;

src/service/oauth/pkce.rs

@@ -1,20 +1,27 @@
+//! PKCE (Proof Key for Code Exchange) verifier/challenge pair generation for OAuth flows.
+
 use base64::{Engine as _, engine::general_purpose::URL_SAFE_NO_PAD};
 use sha2::{Sha256, Digest};
 
 const VERIFIER_LENGTH: usize = 64;
 
+/// A randomly generated, base64url-encoded PKCE code verifier.
 pub struct CodeVerifier(String);
 
 impl CodeVerifier {
+    /// Generate a fresh random code verifier.
     pub fn new() -> Self {
         let bytes: Vec<u8> = (0..VERIFIER_LENGTH).map(|_| rand_byte()).collect();
         CodeVerifier(URL_SAFE_NO_PAD.encode(&bytes))
     }
 
+    /// Borrow the verifier as a string, to send in the token exchange request.
     pub fn as_str(&self) -> &str {
         &self.0
     }
 
+    /// Derive the S256 code challenge (SHA-256 hash, base64url-encoded) to send
+    /// in the authorization request.
     pub fn challenge(&self) -> CodeChallenge {
         let mut hasher = Sha256::new();
         hasher.update(self.0.as_bytes());
@@ -23,6 +30,11 @@ impl CodeVerifier {
     }
 }
 
+/// Produce one pseudo-random byte from the sub-second component of the system clock.
+///
+/// Why: avoids pulling in a `rand` dependency for a short-lived, non-cryptographic
+/// verifier; each byte only needs to be unpredictable enough to prevent code
+/// interception, not cryptographically secure.
 fn rand_byte() -> u8 {
     use std::time::{SystemTime, UNIX_EPOCH};
     let nanos = SystemTime::now()
@@ -35,9 +47,11 @@ fn rand_byte() -> u8 {
     (nanos & 0xFF) as u8
 }
 
+/// The S256-derived code challenge sent in the authorization request URL.
 pub struct CodeChallenge(String);
 
 impl CodeChallenge {
+    /// Borrow the challenge as a string.
     pub fn as_str(&self) -> &str {
         &self.0
     }

src/service/provider.rs

@@ -1,3 +1,6 @@
+//! Blocking HTTP client for OpenAI/Anthropic-compatible chat completion APIs,
+//! supporting both non-streaming and SSE-streaming requests with automatic retry.
+
 use std::time::Duration;
 use anyhow::Result;
 
@@ -12,6 +15,10 @@ pub const DEFAULT_API_KEY: &str = "sk-5dd268d88adb496b-818beb-6bc7498e";
 const CONNECT_TIMEOUT: Duration = Duration::from_secs(10);
 const REQUEST_TIMEOUT: Duration = Duration::from_secs(60);
 
+/// Blocking HTTP client for a single LLM provider endpoint.
+///
+/// Holds the reqwest client, credentials, and model/base URL selection used
+/// by both the non-streaming and streaming chat completion calls.
 pub struct LlmClient {
     pub client: reqwest::blocking::Client,
     pub api_key: String,
@@ -20,6 +27,14 @@ pub struct LlmClient {
 }
 
 impl LlmClient {
+    /// Construct a client, falling back to built-in defaults for empty inputs.
+    ///
+    /// Flow: empty api_key/model → substitute defaults → build reqwest client
+    /// with connect/request timeouts (falling back to an untimed client if
+    /// the builder fails) → normalize base_url.
+    ///
+    /// Why: empty strings are treated as "unset" rather than errors so callers
+    /// can pass through unconfigured settings without special-casing them.
     pub fn new(mut api_key: String, model: String, base_url: Option<String>) -> Self {
         if api_key.is_empty() {
             api_key = DEFAULT_API_KEY.to_string();
@@ -48,6 +63,16 @@ impl LlmClient {
         }
     }
 
+    /// Send a non-streaming chat completion request and return the assistant's reply.
+    ///
+    /// Flow: build request → POST with retry loop (up to 10 attempts, 2s backoff)
+    /// → parse JSON response → extract first choice's message and token usage.
+    ///
+    /// Why: retries transient failures but aborts immediately on 401/403, since
+    /// those indicate a bad API key that retrying won't fix.
+    ///
+    /// Return: `Err` if all retries are exhausted, an auth error occurs, or the
+    /// response has no choices.
     pub fn chat_with_tools_non_streaming(
         &self,
         messages: &[ChatMessage],
@@ -177,6 +202,17 @@ impl LlmClient {
         }
     }
 
+    /// Perform one streaming chat completion request, parsing SSE events until completion.
+    ///
+    /// Flow: POST → read body in chunks → advance past valid UTF-8 boundary →
+    /// feed into `SseParser` → dispatch each `StreamEvent` to `on_event` and
+    /// accumulate in `StreamedTurn` → return assembled assistant message on `Done`.
+    ///
+    /// Why: chunk-by-chunk UTF-8-aware reads avoid splitting multi-byte sequences;
+    /// returns `aborted` error if `on_event` returns false so the caller can cancel.
+    ///
+    /// Return: assembled message + optional usage on success, `Err` on read
+    /// failure, non-2xx status, or callback-initiated abort.
     fn try_stream_once(
         &self,
         req: &ChatRequest,

src/tool/bash_tools.rs

@@ -1,8 +1,12 @@
+//! Tool implementations for interacting with background bash jobs: `bash_output`
+//! and `bash_kill`. Both take a `job_id` produced by `bash` with `run_in_background=true`.
+
 use serde_json::{json, Value};
 use anyhow::{Result, anyhow};
 use super::Tool;
 use super::ToolCtx;
 
+/// Tool: fetch buffered output from a background bash job by `job_id`.
 pub struct BashOutput;
 
 impl Tool for BashOutput {
@@ -39,6 +43,7 @@ impl Tool for BashOutput {
     }
 }
 
+/// Tool: terminate a running background bash job by `job_id`.
 pub struct BashKill;
 
 impl Tool for BashKill {

src/tool/fs/delete.rs

@@ -1,3 +1,5 @@
+//! Tool: `delete` — remove a file or empty directory relative to a workspace root.
+
 use std::fs;
 use std::path::PathBuf;
 use serde_json::{json, Value};
@@ -7,6 +9,7 @@ use super::super::ToolCtx;
 use super::super::resolve_path;
 use super::helpers::arg_str;
 
+/// Tool: delete a file or empty directory. Refuses non-empty directories.
 pub struct Delete;
 
 impl Tool for Delete {
@@ -31,6 +34,10 @@ impl Tool for Delete {
         })
     }
 
+    /// Delete a file or empty directory. Returns success message or errors on failure.
+    ///
+    /// Flow: resolve path → check existence → check dir/file → remove.
+    /// Only empty directories are deletable (non-empty returns an error).
     fn run(&self, ctx: &ToolCtx, args: &Value) -> Result<String> {
         let rel = arg_str(args, "path")?;
         let path: PathBuf = resolve_path(&ctx.workspaces, &rel)?;

src/tool/fs/edit.rs

@@ -1,3 +1,5 @@
+//! Tool: `edit` — replace a substring in a file with a new string.
+
 use std::fs;
 use std::path::PathBuf;
 use serde_json::{json, Value};
@@ -8,6 +10,7 @@ use super::super::resolve_path;
 use super::super::check_graduated_checks;
 use super::helpers::arg_str;
 
+/// Tool: replace text in a file. Requires the old string to be unique unless `replace_all` is true.
 pub struct Edit;
 
 impl Tool for Edit {
@@ -48,6 +51,13 @@ impl Tool for Edit {
         })
     }
 
+    /// Perform the in-file string replacement.
+    ///
+    /// Flow: validate args → resolve path → read file → count occurrences →
+    /// replace one or all → write back → report byte delta (+ optional graduated checks).
+    ///
+    /// Why: requires a non-empty `reason` and a non-empty `old` string to prevent
+    /// accidental identity edits. Enforces uniqueness unless `replace_all` is set.
     fn run(&self, ctx: &ToolCtx, args: &Value) -> Result<String> {
         let rel = arg_str(args, "path")?;
         let old = arg_str(args, "old")?;

src/tool/fs/helpers.rs

@@ -1,7 +1,14 @@
+//! Shared helpers for filesystem tools: extracting string arguments from JSON
+//! and producing user-friendly "not found" diagnostics.
+
 use std::path::Path;
 use serde_json::Value;
 use anyhow::{Result, anyhow};
 
+/// Extract a required string argument from a JSON args map.
+///
+/// Return: the value as `String` if present and a string type; `Err` if missing
+/// or of a different JSON type (null, number, boolean, array, object).
 pub fn arg_str(args: &Value, name: &str) -> Result<String> {
     args.get(name)
         .and_then(|v| v.as_str())
@@ -9,6 +16,12 @@ pub fn arg_str(args: &Value, name: &str) -> Result<String> {
         .ok_or_else(|| anyhow!("missing required argument: {}", name))
 }
 
+/// Produce a user-friendly diagnostic string when a path doesn't resolve or exist.
+///
+/// Checks whether the resolved path canonically falls inside any workspace root
+/// and reports either "path outside workspaces" or "path does not exist" accordingly.
+///
+/// Return: a one-line description of the resolution failure.
 pub fn not_found_help(ctx: &super::super::ToolCtx, path: &Path, rel: &str) -> String {
     let canon = path.canonicalize().unwrap_or_else(|_| path.to_path_buf());
     let in_ws = ctx.workspaces.iter().any(|w| {

src/tool/fs/mod.rs

@@ -1,3 +1,6 @@
+//! Filesystem tool implementations: read, write, edit, and delete operations
+//! on workspace-rooted paths.
+
 pub mod delete;
 pub mod edit;
 pub mod helpers;

src/tool/fs/read.rs

@@ -1,3 +1,5 @@
+//! Tool: `read` — display file contents with line numbers.
+
 use std::fs;
 use std::path::PathBuf;
 use serde_json::{json, Value};
@@ -7,6 +9,7 @@ use super::super::ToolCtx;
 use super::super::resolve_path;
 use super::helpers::{arg_str, not_found_help};
 
+/// Tool: read a file and display it with line numbers, optionally truncated to `limit` lines.
 pub struct Read;
 
 impl Tool for Read {
@@ -35,6 +38,13 @@ impl Tool for Read {
         })
     }
 
+    /// Read and display a file with line numbers.
+    ///
+    /// Flow: resolve path → if not found, call `not_found_help` for diagnostic →
+    /// read entire file → enumerate and format lines → optionally truncate by `limit`.
+    ///
+    /// Return: line-numbered content; `not_found_help` message if the path doesn't
+    /// exist; a "is a directory" message if the path points at a directory.
     fn run(&self, ctx: &ToolCtx, args: &Value) -> Result<String> {
         let rel = arg_str(args, "path")?;
         let limit = args.get("limit").and_then(|v| v.as_u64()).map(|v| v as usize);

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")?;

src/tool/git_cred.rs

@@ -1,9 +1,12 @@
+//! Tool wrapper around `git credential` for store/get/erase operations.
+
 use serde_json::{json, Value};
 use anyhow::{Result, anyhow};
 use std::process::Command;
 use super::Tool;
 use super::ToolCtx;
 
+/// Tool that shells out to `git credential <op>` to store, retrieve, or erase credentials.
 pub struct GitCred;
 
 impl Tool for GitCred {
@@ -29,6 +32,15 @@ impl Tool for GitCred {
         })
     }
 
+    /// Run `git credential <operation>`, forwarding stdin-less invocation to the git binary.
+    ///
+    /// Flow: extract `operation` arg → spawn `git credential <operation>` → capture output.
+    ///
+    /// Why: `store`/`get`/`erase` are the only credential-helper subcommands git supports;
+    /// no stdin is piped, so this mainly surfaces helper output/errors rather than
+    /// performing an interactive credential exchange.
+    ///
+    /// Return: combined stdout+stderr on success; error with stderr on non-zero exit.
     fn run(&self, _ctx: &ToolCtx, args: &Value) -> Result<String> {
         let operation = args.get("operation")
             .and_then(|v| v.as_str())

src/tool/git_operator.rs

@@ -1,9 +1,12 @@
+//! Generic tool for running arbitrary git subcommands.
+
 use std::process::Command;
 use serde_json::{json, Value};
 use anyhow::{Result, anyhow};
 use super::Tool;
 use super::ToolCtx;
 
+/// Tool that runs `git <operation> [args...]` and returns combined stdout/stderr.
 pub struct GitOperator;
 
 impl Tool for GitOperator {
@@ -33,6 +36,16 @@ impl Tool for GitOperator {
         })
     }
 
+    /// Run `git <operation> [args...]` and return its combined output.
+    ///
+    /// Flow: extract `operation` + `args` → spawn `git <operation> <args>` → trim and
+    ///       join stdout/stderr.
+    ///
+    /// Why: no allowlist here — the model may run any git subcommand; destructive
+    /// operations are blocked upstream by `shell_filter::git`, not by this tool.
+    ///
+    /// Return: trimmed combined output on success; error including exit code and
+    /// stderr on failure.
     fn run(&self, _ctx: &ToolCtx, args: &Value) -> Result<String> {
         let operation = args.get("operation")
             .and_then(|v| v.as_str())

src/tool/git_worktree.rs

@@ -1,9 +1,12 @@
+//! Tool for creating git worktrees under the session's worktrees directory.
+
 use std::process::Command;
 use serde_json::{json, Value};
 use anyhow::{Result, anyhow};
 use super::Tool;
 use super::ToolCtx;
 
+/// Tool that creates a new git worktree (`git worktree add`) from a given base ref.
 pub struct GitWorktree;
 
 impl Tool for GitWorktree {
@@ -32,6 +35,13 @@ impl Tool for GitWorktree {
         })
     }
 
+    /// Create the worktree directory and run `git worktree add --checkout <path> <base_ref>`.
+    ///
+    /// Flow: extract name/base_ref → create worktree dir under `ctx.worktrees_dir` →
+    ///       spawn `git worktree add` → combine stdout/stderr.
+    ///
+    /// Return: success message with combined output on success; error including exit
+    /// code and stderr on failure.
     fn run(&self, ctx: &ToolCtx, args: &Value) -> Result<String> {
         let name = args.get("name")
             .and_then(|v| v.as_str())

src/tool/memory/forget.rs

@@ -1,9 +1,12 @@
+//! Tool for deleting a persisted memory entry by name.
+
 use serde_json::{json, Value};
 use anyhow::{Result, anyhow};
 use super::super::Tool;
 use super::super::ToolCtx;
 use crate::model::memory::Memory;
 
+/// Tool that removes a single memory entry from `ctx.memory_dir` by exact name.
 pub struct Forget;
 
 impl Tool for Forget {
@@ -28,6 +31,12 @@ impl Tool for Forget {
         })
     }
 
+    /// Delete the memory file matching `name` from disk.
+    ///
+    /// Flow: extract `name` → `Memory::remove` → confirmation string.
+    ///
+    /// Return: confirmation message on success; error if the memory does not exist
+    /// or the file could not be removed.
     fn run(&self, ctx: &ToolCtx, args: &Value) -> Result<String> {
         let name = args.get("name")
             .and_then(|v| v.as_str())