feat: update README and documentation for new tools and features

- Updated README.md to reflect the addition of 3 new built-in tools, bringing the total to 37.
- Revised architecture documentation to indicate the increase in tool count.
- Enhanced backend documentation with updated line counts for various modules.
- Modified data documentation to change edit log format from JSON to JSONL.
- Updated dependencies documentation to reflect version upgrades for several crates.
- Improved prompts for auto-reviewer, division implementer, planner, tester, and quality reviewer to enforce stricter coding standards regarding linter bypasses.
- Refactored code in various modules to improve clarity and performance, including updates to error handling and tool execution logic.
- Added comprehensive tests for IPC frame serialization and deserialization.

src/app/workflow/company.rs

@@ -93,13 +93,14 @@ fn make_division_phase(
 /// context to flow through the pipeline.
 ///
 /// Returns a consolidated executive summary string.
+#[allow(clippy::ref_option)]
 pub fn run_company_pipeline(
     user_request: &str,
     session_dir: &std::path::Path,
     workspaces: &[std::path::PathBuf],
     turn_events: Option<&Arc<Mutex<std::collections::VecDeque<crate::app::state::runtime::TurnEvent>>>>,
     abort_flag: &Option<Arc<AtomicBool>>,
-    custom_specialists: HashMap<String, Vec<(String, String)>>,
+    custom_specialists: &HashMap<String, Vec<(String, String)>>,
 ) -> anyhow::Result<String> {
     let divisions = division::all_divisions();
 
@@ -179,20 +180,21 @@ pub fn run_company_pipeline(
         .map(|f| f.clone())
         .unwrap_or_default();
 
-    Ok(build_executive_summary(user_request, &results, &all_findings, &divisions, &custom_specialists))
+    Ok(build_executive_summary(user_request, &results, &all_findings, &divisions, custom_specialists))
 }
 
 /// Run a quick company pipeline that skips non-essential divisions
 /// for simple tasks. Flow: Strategy → Engineering → Quality.
 ///
 /// This is for smaller tasks where security audit and full docs are overkill.
+#[allow(clippy::ref_option)]
 pub fn run_company_pipeline_quick(
     user_request: &str,
     session_dir: &std::path::Path,
     workspaces: &[std::path::PathBuf],
     turn_events: Option<&Arc<Mutex<std::collections::VecDeque<crate::app::state::runtime::TurnEvent>>>>,
     abort_flag: &Option<Arc<AtomicBool>>,
-    custom_specialists: HashMap<String, Vec<(String, String)>>,
+    custom_specialists: &HashMap<String, Vec<(String, String)>>,
 ) -> anyhow::Result<String> {
     let divisions = division::all_divisions();
     let quick_divisions = &divisions[..3];
@@ -252,7 +254,7 @@ pub fn run_company_pipeline_quick(
         .map(|f| f.clone())
         .unwrap_or_default();
 
-    Ok(build_executive_summary(user_request, &results, &all_findings, quick_divisions, &custom_specialists))
+    Ok(build_executive_summary(user_request, &results, &all_findings, quick_divisions, custom_specialists))
 }
 
 /// Build a compressed executive summary from pipeline results.
@@ -277,8 +279,7 @@ fn build_executive_summary(
     let mut start_index = 0;
     for div in divisions {
         let count = custom_specialists.get(div.name)
-            .map(Vec::len)
-            .unwrap_or(0);
+            .map_or(0, Vec::len);
 
         let mut division_verdicts = Vec::new();
         for offset in 0..count {
@@ -393,7 +394,7 @@ mod tests {
                 ("Custom Label".to_string(), "Custom Focus Description".to_string())
             ]
         );
-        let specs = make_division_specialists(div, "Test Request", &custom.get("Strategy").unwrap());
+        let specs = make_division_specialists(div, "Test Request", custom.get("Strategy").unwrap());
         assert_eq!(specs.len(), 1);
         if let ScriptPrimitive::Agent(prompt) = &specs[0] {
             assert!(prompt.contains("Custom Label"));

src/app/workflow/engine.rs

@@ -98,7 +98,7 @@ pub type LiveStateFn = Arc<dyn Fn(String, String, AgentStatus) + Send + Sync>;
 /// a stuck stage from blocking the entire pipeline forever.
 ///
 /// Return: the agent's text output, or an error on failure.
-#[allow(clippy::too_many_lines, clippy::too_many_arguments)]
+#[allow(clippy::too_many_lines, clippy::too_many_arguments, clippy::ref_option)]
 fn spawn_single_agent(
     agent_id: &str,
     agent_name: &str,
@@ -185,7 +185,7 @@ fn spawn_single_agent(
     // Link the shared findings Arc so note_finding calls within this
     // subagent write into the same vec visible to sibling agents.
     ctx.workflow_findings = Some(findings.clone());
-    ctx.abort_flag = abort_flag.clone();
+    ctx.abort_flag.clone_from(abort_flag);
 
     // Create an mpsc channel and drain events in a background thread.
     // The drain thread also pushes intra-division progress updates to the
@@ -269,34 +269,30 @@ fn spawn_single_agent(
         let deadline = Duration::from_millis(timeout);
         let mut elapsed = Duration::ZERO;
         loop {
-            match done_rx.recv_timeout(poll_interval) {
-                Ok(r) => break r,
-                Err(_) => {
-                    elapsed += poll_interval;
-                    if elapsed >= deadline {
-                        break Err(anyhow::anyhow!(
-                            "subagent '{bg_name}' timed out after {timeout}ms",
-                        ));
-                    }
-                    if bg_abort.as_ref().is_some_and(|f| f.load(Ordering::SeqCst)) {
-                        break Err(anyhow::anyhow!(
-                            "subagent '{bg_name}' aborted by user",
-                        ));
-                    }
-                }
+            if let Ok(r) = done_rx.recv_timeout(poll_interval) {
+                break r;
+            }
+            elapsed += poll_interval;
+            if elapsed >= deadline {
+                break Err(anyhow::anyhow!(
+                    "subagent '{bg_name}' timed out after {timeout}ms",
+                ));
+            }
+            if bg_abort.as_ref().is_some_and(|f| f.load(Ordering::SeqCst)) {
+                break Err(anyhow::anyhow!(
+                    "subagent '{bg_name}' aborted by user",
+                ));
             }
         }
     } else {
         loop {
-            match done_rx.recv_timeout(poll_interval) {
-                Ok(r) => break r,
-                Err(_) => {
-                    if bg_abort.as_ref().is_some_and(|f| f.load(Ordering::SeqCst)) {
-                        break Err(anyhow::anyhow!(
-                            "subagent '{bg_name}' aborted by user",
-                        ));
-                    }
-                }
+            if let Ok(r) = done_rx.recv_timeout(poll_interval) {
+                break r;
+            }
+            if bg_abort.as_ref().is_some_and(|f| f.load(Ordering::SeqCst)) {
+                break Err(anyhow::anyhow!(
+                    "subagent '{bg_name}' aborted by user",
+                ));
             }
         }
     };
@@ -358,6 +354,7 @@ type ParallelResult = (usize, anyhow::Result<Vec<String>>);
 /// Return: a `Vec<String>` of all agent outputs (or error strings) in
 /// the order they were submitted.
 #[allow(clippy::too_many_arguments)]
+#[allow(clippy::ref_option, clippy::too_many_lines)]
 pub fn execute_primitive(
     primitive: &ScriptPrimitive,
     args: &HashMap<String, String>,
@@ -529,6 +526,7 @@ pub fn run_workflow(
 /// `spawn_agents` invocations remain fully isolated.
 ///
 /// Return: a human-readable summary string.
+#[allow(clippy::ref_option)]
 pub fn run_workflow_tracked(
     script: &WorkflowScript,
     args: &HashMap<String, String>,