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"));