diff --git a/.gitignore b/.gitignore
index 8dd4e44..be63506 100644
--- a/.gitignore
+++ b/.gitignore
@@ -15,3 +15,4 @@ dpg_layout.ini
 tests/temp_workspace
 .mypy_cache
 .slop_cache
+sdm_report_refined.json
diff --git a/scripts/sdm_injector.py b/scripts/sdm_injector.py
new file mode 100644
index 0000000..d4bf8d0
--- /dev/null
+++ b/scripts/sdm_injector.py
@@ -0,0 +1,173 @@
+import ast
+import json
+import os
+import pathlib
+import sys
+import re
+from typing import List, Dict, Any, Optional, Tuple
+
+def find_closing_quotes_pos(line: str) -> Tuple[int, str]:
+ pos_double = line.rfind('"""')
+ pos_single = line.rfind("'''")
+ if pos_double != -1 and pos_single != -1:
+  if pos_double > pos_single: return pos_double, '"""'
+  else: return pos_single, "'''"
+ elif pos_double != -1:
+  return pos_double, '"""'
+ elif pos_single != -1:
+  return pos_single, "'''"
+ return -1, ""
+
+class SdmDocstringInjectorVisitor(ast.NodeVisitor):
+ def __init__(self, file_path: str, sdm_tags_map: Dict[str, Any], lines: List[str]):
+  self.file_path = file_path
+  self.sdm_tags_map = sdm_tags_map
+  self.lines = lines
+  self.targets_to_modify = []
+  self.current_class_name = None
+  self.project_root = pathlib.Path.cwd().resolve()
+
+ def get_rel_path(self, path):
+  p = pathlib.Path(path).resolve()
+  try:
+   return str(p.relative_to(self.project_root)).replace("\\", "/")
+  except (ValueError, RuntimeError):
+   return str(p).replace("\\", "/")
+
+ def _get_sdm_tags(self, name: str, node_type: str, parent_class_name: Optional[str] = None) -> List[str]:
+  relative_file_path = self.get_rel_path(self.file_path)
+  file_data = self.sdm_tags_map.get(relative_file_path)
+  if not file_data: return []
+  tags = []
+  if node_type == 'ClassDef':
+   class_data = file_data.get('classes', {}).get(name, {})
+   class_tag = class_data.get('class_tag')
+   if class_tag: tags.append(class_tag)
+  elif node_type in ('FunctionDef', 'AsyncFunctionDef'):
+   if parent_class_name:
+    class_data = file_data.get('classes', {}).get(parent_class_name, {})
+    tag = class_data.get('methods', {}).get(name)
+    if tag: tags.append(tag)
+   else:
+    tag = file_data.get('functions', {}).get(name)
+    if tag: tags.append(tag)
+  return tags
+
+ def _process_node(self, node, node_type: str):
+  if not node.body: return
+  sdm_tags = self._get_sdm_tags(node.name, node_type, self.current_class_name)
+  first_body_node = node.body[0]
+  if (node.lineno == first_body_node.lineno): return
+  
+  docstring_node = None
+  if isinstance(node.body[0], ast.Expr) and \
+     isinstance(node.body[0].value, ast.Constant) and isinstance(node.body[0].value.value, str):
+   docstring_node = node.body[0].value
+  
+  # Use col_offset of the first body node for exact matching
+  body_indent_count = first_body_node.col_offset
+  
+  if docstring_node:
+   self.targets_to_modify.append({
+    'type': 'append', 'node': node, 'name': node.name, 'sdm_tags': sdm_tags,
+    'start_lineno': docstring_node.lineno, 'end_lineno': docstring_node.end_lineno,
+    'indent_count': body_indent_count, 'existing_doc': docstring_node.value
+   })
+  elif sdm_tags:
+   self.targets_to_modify.append({
+    'type': 'new', 'node': node, 'name': node.name, 'sdm_tags': sdm_tags,
+    'insert_lineno': first_body_node.lineno, 'indent_count': body_indent_count
+   })
+
+ def visit_ClassDef(self, node):
+  self._process_node(node, 'ClassDef')
+  old_class = self.current_class_name
+  self.current_class_name = node.name
+  self.generic_visit(node)
+  self.current_class_name = old_class
+
+ def visit_FunctionDef(self, node):
+  self._process_node(node, 'FunctionDef')
+  self.generic_visit(node)
+
+ def visit_AsyncFunctionDef(self, node):
+  self._process_node(node, 'AsyncFunctionDef')
+  self.generic_visit(node)
+
+def strip_tags(docstring: str) -> str:
+ lines = docstring.splitlines()
+ new_lines = []
+ for line in lines:
+  if re.search(r'\[C:.*\]|\[M:.*\]|\[U:.*\]|\[VARS:.*\]', line): continue
+  new_lines.append(line)
+ while new_lines and not new_lines[-1].strip(): new_lines.pop()
+ return "\n".join(new_lines)
+
+def process_file(py_file_path: pathlib.Path, sdm_tags_map):
+ try:
+  with open(py_file_path, 'r', encoding='utf-8') as f: content = f.read()
+  lines = content.splitlines()
+  if not lines: return
+  try: tree = ast.parse(content)
+  except SyntaxError: return
+  visitor = SdmDocstringInjectorVisitor(str(py_file_path.resolve()), sdm_tags_map, lines)
+  visitor.visit(tree)
+  if not visitor.targets_to_modify: return
+  visitor.targets_to_modify.sort(key=lambda t: t['node'].lineno, reverse=True)
+  modified_lines = lines[:]
+  file_modified = False
+  for target in visitor.targets_to_modify:
+   sdm_tags = target['sdm_tags']
+   indent = " " * target['indent_count']
+   if target['type'] == 'append':
+    clean_doc = strip_tags(target['existing_doc'])
+    if sdm_tags:
+     prepared_tags = [f"{indent}{line}" for t in sdm_tags for line in t.splitlines()]
+     new_content = (clean_doc + "\n" + "\n".join(prepared_tags)) if clean_doc.strip() else "\n".join(prepared_tags)
+    else:
+     new_content = clean_doc
+    start_idx = target['start_lineno'] - 1
+    end_idx = target['end_lineno'] - 1
+    first_line, last_line = modified_lines[start_idx], modified_lines[end_idx]
+    q_start_pos = first_line.find('"""')
+    if q_start_pos == -1: q_start_pos = first_line.find("'''")
+    q_end_pos, q_type = find_closing_quotes_pos(last_line)
+    if q_start_pos != -1 and q_end_pos != -1:
+     q_prefix, q_suffix = first_line[:q_start_pos + 3], last_line[q_end_pos:]
+     if "\n" in new_content or (start_idx != end_idx):
+      replacement = [q_prefix] + [f"{indent}{l}" for l in new_content.splitlines()] + [f"{indent}{q_suffix}"]
+     else:
+      replacement = [f"{q_prefix}{new_content}{q_suffix}"]
+     modified_lines[start_idx:end_idx+1] = replacement
+     file_modified = True
+   elif sdm_tags:
+    prepared_tags = [f"{indent}{line}" for t in sdm_tags for line in t.splitlines()]
+    new_doc = [f'{indent}"""', "\n".join(prepared_tags), f'{indent}"""']
+    insert_idx = target['insert_lineno'] - 1
+    while insert_idx > 0 and not modified_lines[insert_idx-1].strip(): insert_idx -= 1
+    modified_lines[insert_idx:insert_idx] = new_doc
+    file_modified = True
+  if file_modified:
+   with open(py_file_path, 'w', encoding='utf-8') as f: f.write("\n".join(modified_lines))
+ except Exception as e: print(f"Error processing {py_file_path}: {e}", file=sys.stderr)
+
+def main():
+ sdm_report_path = "sdm_report_refined.json"
+ if not pathlib.Path(sdm_report_path).exists():
+  print(f"Error: {sdm_report_path} not found.", file=sys.stderr); sys.exit(1)
+ with open(sdm_report_path, 'r', encoding='utf-8') as f: sdm_tags_map = json.load(f)
+ targets = sys.argv[1:]
+ if not targets:
+  for d in ["src", "simulation", "tests"]:
+   sd = pathlib.Path(d)
+   if sd.exists():
+    for f in sd.rglob("*.py"): process_file(f, sdm_tags_map)
+ else:
+  for t in targets:
+   tp = pathlib.Path(t)
+   if tp.is_file(): process_file(tp, sdm_tags_map)
+   elif tp.is_dir():
+    for f in tp.rglob("*.py"): process_file(f, sdm_tags_map)
+
+if __name__ == "__main__":
+ main()
diff --git a/scripts/sdm_mapper.py b/scripts/sdm_mapper.py
new file mode 100644
index 0000000..2e39844
--- /dev/null
+++ b/scripts/sdm_mapper.py
@@ -0,0 +1,206 @@
+import ast
+import os
+import json
+import sys
+import pathlib
+
+class SDMMapper:
+ def __init__(self):
+  self.files = {} # path -> {"functions": {}, "classes": {}}
+  self.functions_global = {} # name -> {"file": str, "class": str, "callers": set()}
+  self.current_file = ""
+  self.current_class = None
+  self.current_function = None
+  self.project_root = pathlib.Path.cwd().resolve()
+
+ def get_rel_path(self, path):
+  p = pathlib.Path(path).resolve()
+  try:
+   return str(p.relative_to(self.project_root)).replace("\\", "/")
+  except (ValueError, RuntimeError):
+   return str(p).replace("\\", "/")
+
+ def collect_symbols(self, dirs):
+  for d in dirs:
+   if not os.path.exists(d): continue
+   for root, _, files in os.walk(d):
+    for f in files:
+     if f.endswith(".py"):
+      path = os.path.join(root, f)
+      rel_path = self.get_rel_path(path)
+      try:
+       with open(path, "r", encoding="utf-8-sig") as file:
+        tree = ast.parse(file.read(), filename=path)
+        if rel_path not in self.files:
+         self.files[rel_path] = {"functions": {}, "classes": {}}
+        
+        for node in ast.walk(tree):
+         if isinstance(node, (ast.FunctionDef, ast.AsyncFunctionDef)):
+          full_name = node.name
+          # In first pass, we just note definitions. 
+          # Class-member identification happens in visit_ClassDef.
+          pass
+         elif isinstance(node, ast.ClassDef):
+          if node.name not in self.files[rel_path]["classes"]:
+           self.files[rel_path]["classes"][node.name] = {"methods": {}, "variables": {}}
+      except Exception as e:
+       print(f"Error collecting symbols from {path}: {e}", file=sys.stderr)
+
+ def analyze_files(self, dirs):
+  for d in dirs:
+   if not os.path.exists(d): continue
+   for root, _, files in os.walk(d):
+    for f in files:
+     if f.endswith(".py"):
+      self.analyze_file(os.path.join(root, f))
+
+ def analyze_file(self, path):
+  self.current_file = self.get_rel_path(path)
+  if self.current_file not in self.files:
+   self.files[self.current_file] = {"functions": {}, "classes": {}}
+  
+  try:
+   with open(path, "r", encoding="utf-8-sig") as file:
+    tree = ast.parse(file.read(), filename=path)
+    visitor = SDMVisitor(self)
+    visitor.visit(tree)
+  except Exception as e:
+   print(f"Error analyzing {path}: {e}", file=sys.stderr)
+
+class SDMVisitor(ast.NodeVisitor):
+ def __init__(self, mapper):
+  self.mapper = mapper
+  self.current_class = None
+  self.current_function = None
+
+ def visit_ClassDef(self, node):
+  old_class = self.current_class
+  self.current_class = node.name
+  if self.current_class not in self.mapper.files[self.mapper.current_file]["classes"]:
+   self.mapper.files[self.mapper.current_file]["classes"][self.current_class] = {"methods": {}, "variables": {}}
+  self.generic_visit(node)
+  self.current_class = old_class
+
+ def visit_FunctionDef(self, node):
+  old_func = self.current_function
+  self.current_function = node.name
+  
+  full_name = f"{self.current_class}.{node.name}" if self.current_class else node.name
+  if full_name not in self.mapper.functions_global:
+   self.mapper.functions_global[full_name] = {
+    "file": self.mapper.current_file,
+    "class": self.current_class,
+    "callers": set()
+   }
+  
+  self.generic_visit(node)
+  self.current_function = old_func
+
+ def visit_AsyncFunctionDef(self, node):
+  self.visit_FunctionDef(node)
+
+ def visit_Call(self, node):
+  name = None
+  if isinstance(node.func, ast.Name):
+   name = node.func.id
+  elif isinstance(node.func, ast.Attribute):
+   name = node.func.attr
+  
+  if name:
+   # Try to find if it's a known function/method
+   potential_matches = [n for n in self.mapper.functions_global if n == name or n.endswith("." + name)]
+   for match in potential_matches:
+    match_file = self.mapper.functions_global[match]["file"]
+    # EXTERNAL FILTER: Only add caller if it's from a different file
+    if match_file != self.mapper.current_file:
+     caller_name = f"{self.current_class}.{self.current_function}" if self.current_class else (self.current_function or "module")
+     # Include file name for external clarity
+     self.mapper.functions_global[match]["callers"].add(f"{self.mapper.current_file}:{caller_name}")
+  
+  self.generic_visit(node)
+
+ def visit_Attribute(self, node):
+  if isinstance(node.value, ast.Name) and node.value.id == "self" and self.current_class:
+   attr_name = node.attr
+   class_data = self.mapper.files[self.mapper.current_file]["classes"][self.current_class]
+   if attr_name not in class_data["variables"]:
+    class_data["variables"][attr_name] = {"mutations": [], "usages": set()}
+   
+   if isinstance(node.ctx, ast.Store):
+    class_data["variables"][attr_name]["mutations"].append({
+     "file": self.mapper.current_file,
+     "line": node.lineno,
+     "method": self.current_function
+    })
+   elif isinstance(node.ctx, ast.Load):
+    class_data["variables"][attr_name]["usages"].add(self.mapper.current_file)
+  self.generic_visit(node)
+
+def main():
+ target = "."
+ if len(sys.argv) > 1:
+  target = sys.argv[1]
+ 
+ mapper = SDMMapper()
+ dirs = ["src", "simulation", "tests"]
+ 
+ if os.path.isfile(target):
+  mapper.collect_symbols(dirs)
+  mapper.analyze_file(target)
+ else:
+  search_dirs = [target] if target in dirs else dirs
+  mapper.collect_symbols(search_dirs)
+  mapper.analyze_files(search_dirs)
+
+ # Build the final grouped report
+ report = {}
+ 
+ # 1. Add functions/methods
+ for full_name, data in mapper.functions_global.items():
+  f_path = data["file"]
+  if f_path not in report: report[f_path] = {"functions": {}, "classes": {}}
+  
+  # External callers only
+  callers = sorted(list(data["callers"]))
+  if not callers:
+   continue
+
+  tag = f"[C: {', '.join(callers)}]"
+  if data["class"]:
+   c_name = data["class"]
+   if c_name not in report[f_path]["classes"]:
+    report[f_path]["classes"][c_name] = {"methods": {}, "variables": {}}
+   m_name = full_name.split(".")[-1]
+   report[f_path]["classes"][c_name]["methods"][m_name] = tag
+  else:
+   report[f_path]["functions"][full_name] = tag
+
+ # 2. Add class variables
+ for f_path, f_data in mapper.files.items():
+  if f_path not in report: continue
+  for c_name, c_data in f_data["classes"].items():
+   if c_name not in report[f_path]["classes"]: 
+    report[f_path]["classes"][c_name] = {"methods": {}, "variables": {}}
+   
+   class_vars_summary = []
+   for v_name, v_data in c_data["variables"].items():
+    # EXTERNAL FILTER: Only include mutations/usages from different files
+    ext_muts = [f"{m['file']}:{m['line']}, {m['method']}" for m in v_data["mutations"] if m['file'] != f_path]
+    ext_usages = [u for u in v_data["usages"] if u != f_path]
+    
+    if not ext_muts and not ext_usages:
+     continue
+
+    m_tag = f"[M: {'; '.join(ext_muts or ['None'])}]"
+    u_tag = f"[U: {', '.join(sorted(list(ext_usages or ['None'])))}]"
+    tag = f"{m_tag} {u_tag}"
+    report[f_path]["classes"][c_name]["variables"][v_name] = tag
+    class_vars_summary.append(f"{v_name}: {tag}")
+   
+   if class_vars_summary:
+    report[f_path]["classes"][c_name]["class_tag"] = "\n".join(class_vars_summary)
+
+ print(json.dumps(report, indent=1))
+
+if __name__ == "__main__":
+ main()
diff --git a/src/aggregate.py b/src/aggregate.py
index 4107fbb..b2fe481 100644
--- a/src/aggregate.py
+++ b/src/aggregate.py
@@ -61,9 +61,10 @@ def resolve_paths(base_dir: Path, entry: str) -> list[Path]:
 
 def build_discussion_section(history: list[Any]) -> str:
  """
-    Builds a markdown section for discussion history.
-    Handles both legacy list[str] and new list[dict].
-    """
+ 
+     Builds a markdown section for discussion history.
+     Handles both legacy list[str] and new list[dict].
+ """
  sections = []
  for i, entry in enumerate(history, start=1):
   if isinstance(entry, dict):
@@ -76,6 +77,9 @@ def build_discussion_section(history: list[Any]) -> str:
  return "\n\n---\n\n".join(sections)
 
 def build_files_section(base_dir: Path, files: list[str | dict[str, Any]]) -> str:
+ """
+ [C: tests/test_tiered_context.py:test_build_files_section_with_dicts]
+ """
  sections = []
  for entry_raw in files:
   if isinstance(entry_raw, dict):
@@ -120,19 +124,21 @@ def build_screenshots_section(base_dir: Path, screenshots: list[str]) -> str:
 
 def build_file_items(base_dir: Path, files: list[str | dict[str, Any]]) -> list[dict[str, Any]]:
  """
-    Return a list of dicts describing each file, for use by ai_client when it
-    wants to upload individual files rather than inline everything as markdown.
-
-    Each dict has:
-        path           : Path  (resolved absolute path)
-        entry          : str   (original config entry string)
-        content        : str   (file text, or error string)
-        error          : bool
-        mtime          : float (last modification time, for skip-if-unchanged optimization)
-        tier           : int | None (optional tier for context management)
-        auto_aggregate : bool
-        force_full     : bool
-    """
+ 
+     Return a list of dicts describing each file, for use by ai_client when it
+     wants to upload individual files rather than inline everything as markdown.
+ 
+     Each dict has:
+         path           : Path  (resolved absolute path)
+         entry          : str   (original config entry string)
+         content        : str   (file text, or error string)
+         error          : bool
+         mtime          : float (last modification time, for skip-if-unchanged optimization)
+         tier           : int | None (optional tier for context management)
+         auto_aggregate : bool
+         force_full     : bool
+  [C: src/app_controller.py:AppController._bg_task, src/orchestrator_pm.py:module, tests/test_aggregate_flags.py:test_auto_aggregate_skip, tests/test_aggregate_flags.py:test_force_full, tests/test_tiered_context.py:test_build_file_items_with_tiers]
+ """
  with get_monitor().scope("build_file_items"):
   items: list[dict[str, Any]] = []
   for entry_raw in files:
@@ -175,15 +181,19 @@ def build_file_items(base_dir: Path, files: list[str | dict[str, Any]]) -> list[
 
 def build_summary_section(base_dir: Path, files: list[str | dict[str, Any]]) -> str:
  """
-    Build a compact summary section using summarize.py — one short block per file.
-    Used as the initial <context> block instead of full file contents.
-    """
+ 
+     Build a compact summary section using summarize.py — one short block per file.
+     Used as the initial <context> block instead of full file contents.
+ """
  with get_monitor().scope("build_summary_section"):
   items = build_file_items(base_dir, files)
   return summarize.build_summary_markdown(items)
 
 def _build_files_section_from_items(file_items: list[dict[str, Any]]) -> str:
- """Build the files markdown section from pre-read file items (avoids double I/O)."""
+ """
+ Build the files markdown section from pre-read file items (avoids double I/O).
+  [C: tests/test_aggregate_flags.py:test_auto_aggregate_skip, tests/test_ui_summary_only_removal.py:test_aggregate_from_items_respects_auto_aggregate]
+ """
  sections = []
  for item in file_items:
   if not item.get("auto_aggregate", True):
@@ -201,6 +211,9 @@ def _build_files_section_from_items(file_items: list[dict[str, Any]]) -> str:
  return "\n\n---\n\n".join(sections)
 
 def build_beads_section(base_dir: Path) -> str:
+ """
+ [C: tests/test_aggregate_beads.py:test_build_beads_compaction]
+ """
  client = beads_client.BeadsClient(base_dir)
  if not client.is_initialized():
   return ""
@@ -247,20 +260,28 @@ def build_markdown_from_items(file_items: list[dict[str, Any]], screenshot_base_
  return "\n\n---\n\n".join(parts)
 
 def build_markdown_no_history(file_items: list[dict[str, Any]], screenshot_base_dir: Path, screenshots: list[str], summary_only: bool = False, aggregation_strategy: str = "auto") -> str:
- """Build markdown with only files + screenshots (no history). Used for stable caching."""
+ """
+ Build markdown with only files + screenshots (no history). Used for stable caching.
+  [C: src/app_controller.py:AppController._do_generate, tests/test_history_management.py:test_aggregate_blacklist]
+ """
  return build_markdown_from_items(file_items, screenshot_base_dir, screenshots, history=[], summary_only=summary_only, aggregation_strategy=aggregation_strategy)
 
 def build_discussion_text(history: list[str]) -> str:
- """Build just the discussion history section text. Returns empty string if no history."""
+ """
+ Build just the discussion history section text. Returns empty string if no history.
+  [C: src/app_controller.py:AppController._do_generate, tests/test_history_management.py:test_aggregate_includes_segregated_history]
+ """
  if not history:
   return ""
  return "## Discussion History\n\n" + build_discussion_section(history)
 
 def build_tier1_context(file_items: list[dict[str, Any]], screenshot_base_dir: Path, screenshots: list[str], history: list[str]) -> str:
  """
-    Tier 1 Context: Strategic/Orchestration.
-    Full content for core conductor files and files with tier=1, summaries for others.
-    """
+ 
+     Tier 1 Context: Strategic/Orchestration.
+     Full content for core conductor files and files with tier=1, summaries for others.
+  [C: tests/test_aggregate_flags.py:test_auto_aggregate_skip, tests/test_aggregate_flags.py:test_force_full, tests/test_tiered_context.py:test_build_tier1_context_exists, tests/test_tiered_context.py:test_tiered_context_by_tier_field]
+ """
  core_files = {"product.md", "tech-stack.md", "workflow.md", "tracks.md"}
  sections = []
  for item in file_items:
@@ -289,16 +310,20 @@ def build_tier1_context(file_items: list[dict[str, Any]], screenshot_base_dir: P
 
 def build_tier2_context(file_items: list[dict[str, Any]], screenshot_base_dir: Path, screenshots: list[str], history: list[str]) -> str:
  """
-    Tier 2 Context: Architectural/Tech Lead.
-    Full content for all files (standard behavior).
-    """
+ 
+     Tier 2 Context: Architectural/Tech Lead.
+     Full content for all files (standard behavior).
+  [C: tests/test_tiered_context.py:test_build_tier2_context_exists]
+ """
  return build_markdown_from_items(file_items, screenshot_base_dir, screenshots, history, summary_only=False)
 
 def build_tier3_context(file_items: list[dict[str, Any]], screenshot_base_dir: Path, screenshots: list[str], history: list[str], focus_files: list[str]) -> str:
  """
-    Tier 3 Context: Execution/Worker.
-    Full content for focus_files and files with tier=3, summaries/skeletons for others.
-    """
+ 
+     Tier 3 Context: Execution/Worker.
+     Full content for focus_files and files with tier=3, summaries/skeletons for others.
+  [C: tests/test_aggregate_flags.py:test_auto_aggregate_skip, tests/test_aggregate_flags.py:test_force_full, tests/test_perf_aggregate.py:test_build_tier3_context_scaling, tests/test_tiered_context.py:test_build_tier3_context_ast_skeleton, tests/test_tiered_context.py:test_build_tier3_context_exists, tests/test_tiered_context.py:test_tiered_context_by_tier_field]
+ """
  with get_monitor().scope("build_tier3_context"):
   focus_set = set(focus_files)
   parser = ASTParser("python")
@@ -362,6 +387,9 @@ def build_markdown(base_dir: Path, files: list[str | dict[str, Any]], screenshot
   return "\n\n---\n\n".join(parts)
 
 def run(config: dict[str, Any], aggregation_strategy: str = "auto") -> tuple[str, Path, list[dict[str, Any]]]:
+ """
+ [C: simulation/sim_base.py:run_sim, src/ai_client.py:_send_anthropic, src/ai_client.py:_send_deepseek, src/ai_client.py:_send_gemini, src/ai_client.py:_send_gemini_cli, src/ai_client.py:_send_minimax, src/app_controller.py:AppController._cb_start_track, src/app_controller.py:AppController._do_generate, src/app_controller.py:AppController._process_event_queue, src/app_controller.py:AppController._start_track_logic, src/external_editor.py:_find_vscode_in_registry, src/gui_2.py:App._render_snapshot_tab, src/gui_2.py:App.run, src/gui_2.py:main, src/mcp_client.py:get_git_diff, src/project_manager.py:get_git_commit, src/project_manager.py:get_git_log, src/rag_engine.py:RAGEngine._search_mcp, src/shell_runner.py:run_powershell, tests/conftest.py:kill_process_tree, tests/conftest.py:live_gui, tests/test_conductor_abort_event.py:test_conductor_abort_event_populated, tests/test_conductor_engine_v2.py:test_conductor_engine_dynamic_parsing_and_execution, tests/test_conductor_engine_v2.py:test_conductor_engine_run_executes_tickets_in_order, tests/test_extended_sims.py:test_ai_settings_sim_live, tests/test_extended_sims.py:test_context_sim_live, tests/test_extended_sims.py:test_execution_sim_live, tests/test_extended_sims.py:test_tools_sim_live, tests/test_external_editor_gui.py:get_vscode_processes, tests/test_external_editor_gui.py:test_vscode_launches_with_diff_view, tests/test_gui_custom_window.py:test_app_window_is_borderless, tests/test_headless_simulation.py:module, tests/test_headless_verification.py:test_headless_verification_error_and_qa_interceptor, tests/test_headless_verification.py:test_headless_verification_full_run, tests/test_mock_gemini_cli.py:run_mock, tests/test_orchestration_logic.py:test_conductor_engine_run, tests/test_parallel_execution.py:test_conductor_engine_pool_integration, tests/test_sim_ai_settings.py:test_ai_settings_simulation_run, tests/test_sim_context.py:test_context_simulation_run, tests/test_sim_execution.py:test_execution_simulation_run, tests/test_sim_tools.py:test_tools_simulation_run]
+ """
  namespace = config.get("project", {}).get("name")
  if not namespace:
   namespace = config.get("output", {}).get("namespace", "project")
@@ -385,6 +413,9 @@ def run(config: dict[str, Any], aggregation_strategy: str = "auto") -> tuple[str
 
 def main() -> None:
  # Load global config to find active project
+ """
+ [C: simulation/live_walkthrough.py:module, simulation/ping_pong.py:module, src/api_hooks.py:WebSocketServer._run_loop, src/gui_2.py:module, tests/mock_concurrent_mma.py:module, tests/mock_gemini_cli.py:module, tests/test_cli_tool_bridge.py:TestCliToolBridge.test_allow_decision, tests/test_cli_tool_bridge.py:TestCliToolBridge.test_deny_decision, tests/test_cli_tool_bridge.py:TestCliToolBridge.test_unreachable_hook_server, tests/test_cli_tool_bridge.py:module, tests/test_cli_tool_bridge_mapping.py:TestCliToolBridgeMapping.test_mapping_from_api_format, tests/test_cli_tool_bridge_mapping.py:module, tests/test_discussion_takes.py:module, tests/test_external_editor_gui.py:module, tests/test_headless_service.py:TestHeadlessStartup.test_headless_flag_triggers_run, tests/test_headless_service.py:TestHeadlessStartup.test_normal_startup_calls_app_run, tests/test_mma_skeleton.py:module, tests/test_orchestrator_pm.py:module, tests/test_orchestrator_pm_history.py:module, tests/test_post_process.py:module, tests/test_presets.py:module, tests/test_project_serialization.py:module, tests/test_run_worker_lifecycle_abort.py:module, tests/test_symbol_lookup.py:module, tests/test_system_prompt_exposure.py:module, tests/test_theme_nerv_fx.py:module]
+ """
  from src.paths import get_config_path
  config_path = get_config_path()
  if not config_path.exists():
@@ -406,4 +437,3 @@ def main() -> None:
 
 if __name__ == "__main__":
  main()
-
diff --git a/src/app_controller.py b/src/app_controller.py
index a1124a8..b8b0f36 100644
--- a/src/app_controller.py
+++ b/src/app_controller.py
@@ -42,6 +42,9 @@ from src import rag_engine
 from src import theme_2 as theme
 
 def hide_tk_root() -> Tk:
+ """
+ [C: src/gui_2.py:App._render_files_panel, src/gui_2.py:App._render_projects_panel, src/gui_2.py:App._render_provider_panel, src/gui_2.py:App._render_screenshots_panel, src/gui_2.py:App._render_theme_panel, src/gui_2.py:App.render_path_field]
+ """
  root = Tk()
  root.withdraw()
  root.wm_attributes("-topmost", True)
@@ -49,12 +52,17 @@ def hide_tk_root() -> Tk:
 
 def parse_symbols(text: str) -> list[str]:
  """
- Finds all occurrences of '@SymbolName' in text and returns SymbolName.
- SymbolName can be a function, class, or method (e.g. @MyClass, @my_func, @MyClass.my_method).
+ 
+  Finds all occurrences of '@SymbolName' in text and returns SymbolName.
+  SymbolName can be a function, class, or method (e.g. @MyClass, @my_func, @MyClass.my_method).
+  [C: tests/test_symbol_lookup.py:TestSymbolLookup.test_parse_symbols_basic, tests/test_symbol_lookup.py:TestSymbolLookup.test_parse_symbols_edge_cases, tests/test_symbol_lookup.py:TestSymbolLookup.test_parse_symbols_methods, tests/test_symbol_lookup.py:TestSymbolLookup.test_parse_symbols_mixed, tests/test_symbol_lookup.py:TestSymbolLookup.test_parse_symbols_no_symbols]
  """
  return re.findall(r"@([a-zA-Z_][a-zA-Z0-9_]*(?:\.[a-zA-Z_][a-zA-Z0-9_]*)*)", text)
 
 def get_symbol_definition(symbol: str, files: list[str]) -> tuple[str, str, int] | None:
+ """
+ [C: tests/test_symbol_lookup.py:TestSymbolLookup.test_get_symbol_definition_found, tests/test_symbol_lookup.py:TestSymbolLookup.test_get_symbol_definition_not_found]
+ """
  for file_path in files:
   result = mcp_client.py_get_symbol_info(file_path, symbol)
   if isinstance(result, tuple):
@@ -74,6 +82,9 @@ class ConfirmRequest(BaseModel):
 
 class ConfirmDialog:
  def __init__(self, script: str, base_dir: str) -> None:
+  """
+  [C: src/mcp_client.py:_DDGParser.__init__, src/mcp_client.py:_TextExtractor.__init__]
+  """
   self._uid = str(uuid.uuid4())
   self._script = str(script) if script is not None else ""
   self._base_dir = str(base_dir) if base_dir is not None else ""
@@ -82,6 +93,9 @@ class ConfirmDialog:
   self._approved = False
 
  def wait(self) -> tuple[bool, str]:
+  """
+  [C: src/mcp_client.py:StdioMCPServer.stop, src/multi_agent_conductor.py:confirm_execution, src/multi_agent_conductor.py:confirm_spawn, tests/conftest.py:live_gui, tests/test_ai_client_concurrency.py:run_t1, tests/test_ai_client_concurrency.py:run_t2, tests/test_conductor_engine_abort.py:worker, tests/test_parallel_execution.py:test_worker_pool_limit]
+  """
   start_time = time.time()
   with self._condition:
    while not self._done:
@@ -92,12 +106,18 @@ class ConfirmDialog:
 
 class MMAApprovalDialog:
  def __init__(self, ticket_id: str, payload: str) -> None:
+  """
+  [C: src/mcp_client.py:_DDGParser.__init__, src/mcp_client.py:_TextExtractor.__init__]
+  """
   self._payload = payload
   self._condition = threading.Condition()
   self._done = False
   self._approved = False
 
  def wait(self) -> tuple[bool, str]:
+  """
+  [C: src/mcp_client.py:StdioMCPServer.stop, src/multi_agent_conductor.py:confirm_execution, src/multi_agent_conductor.py:confirm_spawn, tests/conftest.py:live_gui, tests/test_ai_client_concurrency.py:run_t1, tests/test_ai_client_concurrency.py:run_t2, tests/test_conductor_engine_abort.py:worker, tests/test_parallel_execution.py:test_worker_pool_limit]
+  """
   start_time = time.time()
   with self._condition:
    while not self._done:
@@ -108,6 +128,9 @@ class MMAApprovalDialog:
 
 class MMASpawnApprovalDialog:
  def __init__(self, ticket_id: str, role: str, prompt: str, context_md: str) -> None:
+  """
+  [C: src/mcp_client.py:_DDGParser.__init__, src/mcp_client.py:_TextExtractor.__init__]
+  """
   self._prompt = prompt
   self._context_md = context_md
   self._condition = threading.Condition()
@@ -116,6 +139,9 @@ class MMASpawnApprovalDialog:
   self._abort = False
 
  def wait(self) -> dict[str, Any]:
+  """
+  [C: src/mcp_client.py:StdioMCPServer.stop, src/multi_agent_conductor.py:confirm_execution, src/multi_agent_conductor.py:confirm_spawn, tests/conftest.py:live_gui, tests/test_ai_client_concurrency.py:run_t1, tests/test_ai_client_concurrency.py:run_t2, tests/test_conductor_engine_abort.py:worker, tests/test_parallel_execution.py:test_worker_pool_limit]
+  """
   start_time = time.time()
   with self._condition:
    while not self._done:
@@ -131,12 +157,16 @@ class MMASpawnApprovalDialog:
 
 class AppController:
  """
- The headless controller for the Manual Slop application.
- Owns the application state and manages background services.
+ 
+  The headless controller for the Manual Slop application.
+  Owns the application state and manages background services.
  """
 
  def __init__(self):
   # Initialize locks first to avoid initialization order issues
+  """
+  [C: src/mcp_client.py:_DDGParser.__init__, src/mcp_client.py:_TextExtractor.__init__]
+  """
   self._send_thread_lock: threading.Lock = threading.Lock()
   self._disc_entries_lock: threading.Lock = threading.Lock()
   self._pending_comms_lock: threading.Lock = threading.Lock()
@@ -486,7 +516,10 @@ class AppController:
   return self.ui_files_base_dir
 
  def _update_inject_preview(self) -> None:
-  """Updates the preview content based on the selected file and injection mode."""
+  """
+  Updates the preview content based on the selected file and injection mode.
+    [C: src/gui_2.py:App._gui_func, tests/test_skeleton_injection.py:test_update_inject_preview_full, tests/test_skeleton_injection.py:test_update_inject_preview_skeleton, tests/test_skeleton_injection.py:test_update_inject_preview_truncation]
+  """
   if not self._inject_file_path:
    self._inject_preview = ""
    return
@@ -720,6 +753,9 @@ class AppController:
 
  def _process_pending_gui_tasks(self) -> None:
   # Periodic telemetry broadcast
+  """
+  [C: src/gui_2.py:App._gui_func, tests/test_api_hook_extensions.py:test_app_processes_new_actions, tests/test_gui_updates.py:test_gui_updates_on_event, tests/test_live_gui_integration_v2.py:test_user_request_error_handling, tests/test_live_gui_integration_v2.py:test_user_request_integration_flow, tests/test_mma_orchestration_gui.py:test_handle_ai_response_fallback, tests/test_mma_orchestration_gui.py:test_handle_ai_response_with_stream_id, tests/test_mma_orchestration_gui.py:test_process_pending_gui_tasks_mma_spawn_approval, tests/test_mma_orchestration_gui.py:test_process_pending_gui_tasks_show_track_proposal, tests/test_process_pending_gui_tasks.py:test_gcli_path_updates_adapter, tests/test_process_pending_gui_tasks.py:test_redundant_calls_in_process_pending_gui_tasks]
+  """
   now = time.time()
   if hasattr(self, 'event_queue') and hasattr(self.event_queue, 'websocket_server') and self.event_queue.websocket_server:
    if now - self._last_telemetry_time >= 1.0:
@@ -918,6 +954,9 @@ class AppController:
        class AutoSpawnDialog:
         def __init__(self, t): self.t = t
         def wait(self):
+         """
+         [C: src/mcp_client.py:StdioMCPServer.stop, src/multi_agent_conductor.py:confirm_execution, src/multi_agent_conductor.py:confirm_spawn, tests/conftest.py:live_gui, tests/test_ai_client_concurrency.py:run_t1, tests/test_ai_client_concurrency.py:run_t2, tests/test_conductor_engine_abort.py:worker, tests/test_parallel_execution.py:test_worker_pool_limit]
+         """
          return {'approved': True, 'abort': False, 'prompt': self.t.get("prompt"), 'context_md': self.t.get("context_md")}
        task["dialog_container"][0] = AutoSpawnDialog(task)
       continue
@@ -987,7 +1026,10 @@ class AppController:
     print(f"Error executing GUI task: {e}")
 
  def _process_pending_history_adds(self) -> None:
-  """Synchronizes pending history entries to the active discussion and project state."""
+  """
+  Synchronizes pending history entries to the active discussion and project state.
+    [C: src/gui_2.py:App._gui_func]
+  """
   with self._pending_history_adds_lock:
    items = self._pending_history_adds[:]
    self._pending_history_adds.clear()
@@ -1012,7 +1054,10 @@ class AppController:
       self.disc_entries.append(item)
 
  def _process_pending_tool_calls(self) -> bool:
-  """Drains pending tool calls into the tool log. Returns True if any were processed."""
+  """
+  Drains pending tool calls into the tool log. Returns True if any were processed.
+    [C: src/gui_2.py:App._gui_func]
+  """
   with self._pending_tool_calls_lock:
    items = self._pending_tool_calls[:]
    self._pending_tool_calls.clear()
@@ -1056,7 +1101,10 @@ class AppController:
     self._pending_dialog = None
 
  def init_state(self):
-  """Initializes the application state from configurations."""
+  """
+  Initializes the application state from configurations.
+    [C: src/gui_2.py:App.__init__, src/gui_2.py:App._render_paths_panel, src/gui_2.py:App._save_paths, tests/test_app_controller_mcp.py:test_app_controller_mcp_loading, tests/test_app_controller_mcp.py:test_app_controller_mcp_project_override, tests/test_external_mcp_e2e.py:test_external_mcp_e2e_refresh_and_call, tests/test_system_prompt_exposure.py:TestSystemPromptExposure.test_app_controller_init_state_loads_prompts]
+  """
   self.active_tickets = []
   self.ui_separate_task_dag = False
   self.ui_separate_usage_analytics = False
@@ -1198,6 +1246,9 @@ class AppController:
   self.event_queue.put('refresh_external_mcps', None)
 
  async def refresh_external_mcps(self):
+  """
+  [C: tests/test_external_mcp_e2e.py:test_external_mcp_e2e_refresh_and_call]
+  """
   await mcp_client.get_external_mcp_manager().stop_all()
   # Start servers with auto_start=True
   for name, cfg in self.mcp_config.mcpServers.items():
@@ -1205,6 +1256,9 @@ class AppController:
     await mcp_client.get_external_mcp_manager().add_server(cfg)
 
  def cb_load_prior_log(self, path: Optional[str] = None) -> None:
+  """
+  [C: src/gui_2.py:App._render_log_management]
+  """
   root = hide_tk_root()
   if path is None:
    path = filedialog.askdirectory(
@@ -1393,6 +1447,9 @@ class AppController:
 
 
  def cb_exit_prior_session(self):
+  """
+  [C: src/gui_2.py:App._render_comms_history_panel, src/gui_2.py:App._render_discussion_panel]
+  """
   self.is_viewing_prior_session = False
   if self._current_session_usage:
    self.session_usage = self._current_session_usage
@@ -1475,6 +1532,9 @@ class AppController:
   thread.start()
 
  def _fetch_models(self, provider: str) -> None:
+  """
+  [C: src/gui_2.py:App.run]
+  """
   self.ai_status = "fetching models..."
 
   def do_fetch() -> None:
@@ -1498,14 +1558,20 @@ class AppController:
   self.models_thread.start()
 
  def start_services(self, app: Any = None):
-  """Starts background threads."""
+  """
+  Starts background threads.
+    [C: src/gui_2.py:App.__init__]
+  """
   self._prune_old_logs()
   self._init_ai_and_hooks(app)
   self._loop_thread = threading.Thread(target=self._run_event_loop, daemon=True)
   self._loop_thread.start()
 
  def shutdown(self) -> None:
-  """Stops background threads and cleans up resources."""
+  """
+  Stops background threads and cleans up resources.
+    [C: src/gui_2.py:App.run, src/gui_2.py:App.shutdown, tests/conftest.py:app_instance, tests/conftest.py:mock_app]
+  """
   from src import ai_client
   ai_client.cleanup()
   if hasattr(self, 'hook_server') and self.hook_server:
@@ -1604,7 +1670,10 @@ class AppController:
     asyncio.run(self.refresh_external_mcps())
 
  def _handle_request_event(self, event: events.UserRequestEvent) -> None:
-  """Processes a UserRequestEvent by calling the AI client."""
+  """
+  Processes a UserRequestEvent by calling the AI client.
+    [C: tests/test_live_gui_integration_v2.py:test_user_request_error_handling, tests/test_live_gui_integration_v2.py:test_user_request_integration_flow, tests/test_rag_integration.py:test_rag_integration]
+  """
   self.ai_status = 'sending...'
   ai_client.set_current_tier(None) # Ensure main discussion is untagged
   # Clear response area for new turn
@@ -1662,6 +1731,9 @@ class AppController:
   self.event_queue.put("response", {"text": text, "status": "streaming...", "role": "AI"})
 
  def _on_comms_entry(self, entry: Dict[str, Any]) -> None:
+  """
+  [C: tests/test_app_controller_offloading.py:test_on_comms_entry_tool_result_offloading]
+  """
   optimized_entry = self._offload_entry_payload(entry)
   session_logger.log_comms(optimized_entry)
   entry["local_ts"] = time.time()
@@ -1756,6 +1828,9 @@ class AppController:
    self._pending_comms.append(entry)
 
  def _on_tool_log(self, script: str, result: str) -> None:
+  """
+  [C: tests/test_app_controller_offloading.py:test_on_tool_log_offloading]
+  """
   session_logger.log_tool_call(script, result, None)
   session_logger.log_tool_output(result)
   source_tier = ai_client.get_current_tier()
@@ -1763,6 +1838,9 @@ class AppController:
    self._pending_tool_calls.append({"script": script, "result": result, "ts": time.time(), "source_tier": source_tier})
 
  def _on_api_event(self, event_name: str = "generic_event", **kwargs: Any) -> None:
+  """
+  [C: tests/test_gui_updates.py:test_gui_updates_on_event]
+  """
   payload = kwargs.get("payload", {})
   # Push to background event queue, NOT GUI queue
   self.event_queue.put("refresh_api_metrics", payload)
@@ -1778,6 +1856,9 @@ class AppController:
    })
 
  def _confirm_and_run(self, script: str, base_dir: str, qa_callback: Optional[Callable[[str], str]] = None, patch_callback: Optional[Callable[[str, str], Optional[str]]] = None) -> Optional[str]:
+  """
+  [C: tests/test_arch_boundary_phase2.py:TestArchBoundaryPhase2.test_mutating_tool_triggers_callback, tests/test_arch_boundary_phase2.py:TestArchBoundaryPhase2.test_rejection_prevents_dispatch]
+  """
   if self.test_hooks_enabled and not getattr(self, "ui_manual_approve", False):
    self.ai_status = "running powershell..."
    output = shell_runner.run_powershell(script, base_dir, qa_callback=qa_callback, patch_callback=patch_callback)
@@ -1815,6 +1896,9 @@ class AppController:
   return output
 
  def _append_tool_log(self, script: str, result: str, source_tier: str | None = None, elapsed_ms: float = 0.0) -> None:
+  """
+  [C: tests/test_mma_agent_focus_phase1.py:test_append_tool_log_dict_has_source_tier, tests/test_mma_agent_focus_phase1.py:test_append_tool_log_dict_keys, tests/test_mma_agent_focus_phase1.py:test_append_tool_log_stores_dict]
+  """
   self._tool_log.append({"script": script, "result": result, "ts": time.time(), "source_tier": source_tier})
   tool_name = self._extract_tool_name(script)
   is_failure = "REJECTED" in result or "Error" in result or "error" in result.lower()
@@ -1910,7 +1994,10 @@ class AppController:
    self._token_stats_dirty = True
 
  def create_api(self) -> FastAPI:
-  """Creates and configures the FastAPI application for headless mode."""
+  """
+  Creates and configures the FastAPI application for headless mode.
+    [C: src/gui_2.py:App.run, tests/test_headless_service.py:TestHeadlessAPI.setUp]
+  """
   api = FastAPI(title="Manual Slop Headless API")
   API_KEY_NAME = "X-API-KEY"
   api_key_header = APIKeyHeader(name=API_KEY_NAME, auto_error=False)
@@ -1934,7 +2021,10 @@ class AppController:
 
   @api.get("/api/gui/state", dependencies=[Depends(get_api_key)])
   def get_gui_state() -> dict[str, Any]:
-   """Returns the current GUI state for specific fields."""
+   """
+   Returns the current GUI state for specific fields.
+      [C: tests/test_ai_settings_layout.py:test_change_provider_via_hook, tests/test_ai_settings_layout.py:test_set_params_via_custom_callback, tests/test_conductor_api_hook_integration.py:simulate_conductor_phase_completion, tests/test_external_editor_gui.py:test_button_click_is_received, tests/test_external_editor_gui.py:test_patch_modal_shows_with_configured_editor, tests/test_external_editor_gui.py:test_vscode_launches_with_diff_view, tests/test_gui_text_viewer.py:test_text_viewer_state_update, tests/test_hooks.py:test_live_hook_server_responses, tests/test_live_gui_integration_v2.py:test_api_gui_state_live, tests/test_live_workflow.py:test_full_live_workflow, tests/test_live_workflow.py:wait_for_value, tests/test_patch_modal_gui.py:test_patch_apply_modal_workflow, tests/test_patch_modal_gui.py:test_patch_modal_appears_on_trigger, tests/test_rag_phase4_final_verify.py:test_phase4_final_verify, tests/test_rag_phase4_stress.py:test_rag_large_codebase_verification_sim, tests/test_saved_presets_sim.py:test_preset_manager_modal, tests/test_saved_presets_sim.py:test_preset_switching, tests/test_task_dag_popout_sim.py:test_task_dag_popout, tests/test_tool_management_layout.py:test_tool_management_gettable_fields, tests/test_tool_management_layout.py:test_tool_management_state_updates, tests/test_tool_presets_sim.py:test_tool_preset_switching, tests/test_usage_analytics_popout_sim.py:test_usage_analytics_popout]
+   """
    gettable = getattr(self, "_gettable_fields", {})
    state = {}
    import dataclasses
@@ -1948,7 +2038,10 @@ class AppController:
 
   @api.get("/api/gui/mma_status", dependencies=[Depends(get_api_key)])
   def get_mma_status() -> dict[str, Any]:
-   """Dedicated endpoint for MMA-related status."""
+   """
+   Dedicated endpoint for MMA-related status.
+      [C: tests/test_headless_simulation.py:test_mma_track_lifecycle_simulation, tests/test_live_workflow.py:test_full_live_workflow, tests/test_mma_concurrent_tracks_sim.py:_poll_mma_status, tests/test_mma_concurrent_tracks_sim.py:test_mma_concurrent_tracks_execution, tests/test_mma_concurrent_tracks_stress_sim.py:test_mma_concurrent_tracks_stress, tests/test_mma_step_mode_sim.py:_poll_mma_status, tests/test_mma_step_mode_sim.py:test_mma_step_mode_approval_flow, tests/test_visual_orchestration.py:test_mma_epic_lifecycle, tests/test_visual_sim_gui_ux.py:test_gui_ux_event_routing, tests/test_visual_sim_mma_v2.py:_poll]
+   """
    return {
     "mma_status": self.mma_status,
     "ai_status": self.ai_status,
@@ -1963,7 +2056,10 @@ class AppController:
 
   @api.post("/api/gui", dependencies=[Depends(get_api_key)])
   def post_gui(req: dict) -> dict[str, str]:
-   """Pushes a GUI task to the event queue."""
+   """
+   Pushes a GUI task to the event queue.
+      [C: tests/test_ai_settings_layout.py:test_set_params_via_custom_callback, tests/test_api_hook_client.py:test_post_gui_success, tests/test_gui2_parity.py:test_gui2_custom_callback_hook_works, tests/test_gui2_parity.py:test_gui2_set_value_hook_works, tests/test_visual_mma.py:test_visual_mma_components]
+   """
    self.event_queue.put("gui_task", req)
    return {"status": "queued"}
 
@@ -1988,7 +2084,10 @@ class AppController:
 
   @api.get("/api/performance", dependencies=[Depends(get_api_key)])
   def get_performance() -> dict[str, Any]:
-   """Returns performance monitor metrics."""
+   """
+   Returns performance monitor metrics.
+      [C: tests/test_gui2_performance.py:test_performance_benchmarking, tests/test_gui_performance_requirements.py:test_idle_performance_requirements, tests/test_gui_stress_performance.py:test_comms_volume_stress_performance, tests/test_selectable_ui.py:test_selectable_label_stability, tests/test_visual_sim_gui_ux.py:test_gui_ux_event_routing]
+   """
    return {"performance": self.perf_monitor.get_metrics()}
 
   @api.get("/api/gui/diagnostics", dependencies=[Depends(get_api_key)])
@@ -2107,7 +2206,10 @@ class AppController:
 
   @api.get("/api/v1/sessions/{session_id}", dependencies=[Depends(get_api_key)])
   def get_session(session_id: str) -> dict[str, Any]:
-   """Returns the content of the comms.log for a specific session."""
+   """
+   Returns the content of the comms.log for a specific session.
+      [C: simulation/ping_pong.py:main, simulation/sim_context.py:ContextSimulation.run, simulation/sim_execution.py:ExecutionSimulation.run, simulation/sim_tools.py:ToolsSimulation.run, simulation/workflow_sim.py:WorkflowSimulator.run_discussion_turn_async, simulation/workflow_sim.py:WorkflowSimulator.wait_for_ai_response, tests/test_api_hook_client.py:test_get_session_success, tests/test_gui_stress_performance.py:test_comms_volume_stress_performance, tests/test_live_workflow.py:test_full_live_workflow, tests/test_rag_phase4_final_verify.py:test_phase4_final_verify, tests/test_rag_phase4_stress.py:test_rag_large_codebase_verification_sim]
+   """
    log_path = paths.get_logs_dir() / session_id / "comms.log"
    if not log_path.exists():
     raise HTTPException(status_code=404, detail="Session log not found")
@@ -2162,15 +2264,24 @@ class AppController:
   self.ai_status = "config saved"
 
  def _cb_reset_base_prompt(self, user_data=None) -> None:
+  """
+  [C: src/gui_2.py:App._render_system_prompts_panel]
+  """
   self.ui_base_system_prompt = ai_client._SYSTEM_PROMPT
   self.ui_use_default_base_prompt = False
 
  def _cb_clear_summary_cache(self, user_data=None) -> None:
+  """
+  [C: src/gui_2.py:App._render_files_panel]
+  """
   from src import summarize
   summarize._summary_cache.clear()
   self._push_mma_state_update()
 
  def _cb_show_base_prompt_diff(self, user_data=None) -> None:
+  """
+  [C: src/gui_2.py:App._render_system_prompts_panel]
+  """
   self._show_base_prompt_diff_modal = True
 
  def _cb_disc_create(self) -> None:
@@ -2180,6 +2291,9 @@ class AppController:
    self.ui_disc_new_name_input = ""
 
  def _switch_project(self, path: str) -> None:
+  """
+  [C: src/gui_2.py:App._render_projects_panel]
+  """
   if not Path(path).exists():
    self.ai_status = f"project file not found: {path}"
    return
@@ -2200,6 +2314,9 @@ class AppController:
 
  def _refresh_from_project(self) -> None:
   # Deserialize FileItems in files.paths
+  """
+  [C: tests/test_mma_dashboard_refresh.py:test_mma_dashboard_initialization_refresh, tests/test_mma_dashboard_refresh.py:test_mma_dashboard_refresh]
+  """
   raw_paths = self.project.get("files", {}).get("paths", [])
   self.files = []
   for p in raw_paths:
@@ -2279,6 +2396,9 @@ class AppController:
    self._rebuild_rag_index()
 
  def _cb_save_workspace_profile(self, name: str, scope: str = 'project') -> None:
+  """
+  [C: src/gui_2.py:App._render_save_workspace_profile_modal]
+  """
   if not hasattr(self, '_app') or not self._app:
    return
   profile = self._app._capture_workspace_profile(name)
@@ -2287,18 +2407,27 @@ class AppController:
   self._app.workspace_profiles = self.workspace_profiles
 
  def _cb_delete_workspace_profile(self, name: str, scope: str = 'project') -> None:
+  """
+  [C: src/gui_2.py:App._show_menus]
+  """
   self.workspace_manager.delete_profile(name, scope=scope)
   self.workspace_profiles = self.workspace_manager.load_all_profiles()
   if hasattr(self, '_app') and self._app:
    self._app.workspace_profiles = self.workspace_profiles
 
  def _cb_load_workspace_profile(self, name: str) -> None:
+  """
+  [C: src/gui_2.py:App._show_menus]
+  """
   if name in self.workspace_profiles:
    profile = self.workspace_profiles[name]
    if hasattr(self, '_app') and self._app:
     self._app._apply_workspace_profile(profile)
 
  def _apply_preset(self, name: str, scope: str) -> None:
+  """
+  [C: src/gui_2.py:App._render_system_prompts_panel]
+  """
   print(f"[DEBUG] _apply_preset: name={name}, scope={scope}")
   if name == "None":
    if scope == "global":
@@ -2318,6 +2447,9 @@ class AppController:
    self.ui_project_preset_name = name
 
  def _cb_save_preset(self, name, content, scope):
+  """
+  [C: src/gui_2.py:App._render_preset_manager_content]
+  """
   print(f"[DEBUG] _cb_save_preset: name={name}, scope={scope}")
   if not name or not name.strip():
    raise ValueError("Preset name cannot be empty or whitespace.")
@@ -2330,19 +2462,31 @@ class AppController:
   print(f"[DEBUG] _cb_save_preset: saved {name}, total presets now {len(self.presets)}")
 
  def _cb_delete_preset(self, name, scope):
+  """
+  [C: src/gui_2.py:App._render_preset_manager_content]
+  """
   self.preset_manager.delete_preset(name, scope)
   self.presets = self.preset_manager.load_all()
 
  def _cb_save_tool_preset(self, name, categories, scope):
+  """
+  [C: src/gui_2.py:App._render_tool_preset_manager_content]
+  """
   preset = models.ToolPreset(name=name, categories=categories)
   self.tool_preset_manager.save_preset(preset, scope)
   self.tool_presets = self.tool_preset_manager.load_all_presets()
 
  def _cb_delete_tool_preset(self, name, scope):
+  """
+  [C: src/gui_2.py:App._render_tool_preset_manager_content]
+  """
   self.tool_preset_manager.delete_preset(name, scope)
   self.tool_presets = self.tool_preset_manager.load_all_presets()
 
  def _cb_save_bias_profile(self, profile: models.BiasProfile, scope: str = "project"):
+  """
+  [C: src/gui_2.py:App._render_tool_preset_manager_content]
+  """
   self.tool_preset_manager.save_bias_profile(profile, scope)
   self.bias_profiles = self.tool_preset_manager.load_all_bias_profiles()
 
@@ -2351,15 +2495,24 @@ class AppController:
   self.bias_profiles = self.tool_preset_manager.load_all_bias_profiles()
 
  def _cb_save_persona(self, persona: models.Persona, scope: str = "project") -> None:
+  """
+  [C: src/gui_2.py:App._render_persona_editor_window]
+  """
   self.persona_manager.save_persona(persona, scope)
   self.personas = self.persona_manager.load_all()
 
  def _cb_delete_persona(self, name: str, scope: str = "project") -> None:
+  """
+  [C: src/gui_2.py:App._render_persona_editor_window]
+  """
   self.persona_manager.delete_persona(name, scope)
   self.personas = self.persona_manager.load_all()
 
 
  def _cb_load_track(self, track_id: str) -> None:
+  """
+  [C: src/gui_2.py:App._render_mma_dashboard]
+  """
   state = project_manager.load_track_state(track_id, self.active_project_root)
   if state:
    try:
@@ -2391,6 +2544,9 @@ class AppController:
     print(f"Error loading track {track_id}: {e}")
 
  def _save_active_project(self) -> None:
+  """
+  [C: src/gui_2.py:App.delete_context_preset, src/gui_2.py:App.save_context_preset]
+  """
   if self.active_project_path:
    try:
     cleaned = project_manager.clean_nones(self.project)
@@ -2399,11 +2555,17 @@ class AppController:
     self.ai_status = f"save error: {e}"
 
  def _get_discussion_names(self) -> list[str]:
+  """
+  [C: src/gui_2.py:App._render_discussion_panel]
+  """
   disc_sec = self.project.get("discussion", {})
   discussions = disc_sec.get("discussions", {})
   return sorted(discussions.keys())
 
  def _switch_discussion(self, name: str) -> None:
+  """
+  [C: src/gui_2.py:App._render_discussion_panel, src/gui_2.py:App._render_takes_panel]
+  """
   self._flush_disc_entries_to_project()
   disc_sec = self.project.get("discussion", {})
   discussions = disc_sec.get("discussions", {})
@@ -2419,6 +2581,9 @@ class AppController:
   self.ai_status = f"discussion: {name}"
 
  def _flush_disc_entries_to_project(self) -> None:
+  """
+  [C: src/gui_2.py:App._render_discussion_panel]
+  """
   history_strings = [project_manager.entry_to_str(e) for e in self.disc_entries]
   if self.active_track and self._track_discussion_active:
    project_manager.save_track_history(self.active_track.id, history_strings, self.active_project_root)
@@ -2430,6 +2595,9 @@ class AppController:
   disc_data["last_updated"] = project_manager.now_ts()
 
  def _create_discussion(self, name: str) -> None:
+  """
+  [C: src/gui_2.py:App._render_discussion_panel, src/gui_2.py:App._render_synthesis_panel, src/gui_2.py:App._render_takes_panel]
+  """
   disc_sec = self.project.setdefault("discussion", {})
   discussions = disc_sec.setdefault("discussions", {})
   if name in discussions:
@@ -2439,6 +2607,9 @@ class AppController:
   self._switch_discussion(name)
 
  def _branch_discussion(self, index: int) -> None:
+  """
+  [C: src/gui_2.py:App._render_discussion_panel]
+  """
   self._flush_disc_entries_to_project()
   # Generate a unique branch name
   base_name = self.active_discussion.split("_take_")[0]
@@ -2453,6 +2624,9 @@ class AppController:
   project_manager.branch_discussion(self.project, self.active_discussion, new_name, index)
   self._switch_discussion(new_name)
  def _rename_discussion(self, old_name: str, new_name: str) -> None:
+  """
+  [C: src/gui_2.py:App._render_discussion_panel]
+  """
   disc_sec = self.project.get("discussion", {})
   discussions = disc_sec.get("discussions", {})
   if old_name not in discussions:
@@ -2466,6 +2640,9 @@ class AppController:
    disc_sec["active"] = new_name
 
  def _delete_discussion(self, name: str) -> None:
+  """
+  [C: src/gui_2.py:App._render_discussion_panel]
+  """
   disc_sec = self.project.get("discussion", {})
   discussions = disc_sec.get("discussions", {})
   if len(discussions) <= 1:
@@ -2479,6 +2656,9 @@ class AppController:
    self._switch_discussion(remaining[0])
 
  def _handle_mma_respond(self, approved: bool, payload: str | None = None, abort: bool = False, prompt: str | None = None, context_md: str | None = None) -> None:
+  """
+  [C: src/gui_2.py:App._gui_func, src/gui_2.py:App._handle_approve_mma_step, src/gui_2.py:App._handle_approve_spawn]
+  """
   if self._pending_mma_approvals:
    task = self._pending_mma_approvals.pop(0)
    dlg = task.get("dialog_container", [None])[0]
@@ -2504,7 +2684,10 @@ class AppController:
      spawn_dlg._condition.notify_all()
 
  def _handle_approve_ask(self) -> None:
-  """Responds with approval for a pending /api/ask request."""
+  """
+  Responds with approval for a pending /api/ask request.
+    [C: src/gui_2.py:App.__init__, src/gui_2.py:App._gui_func]
+  """
   if not self._ask_request_id: return
   request_id = self._ask_request_id
 
@@ -2522,7 +2705,10 @@ class AppController:
   self._ask_tool_data = None
 
  def _handle_reject_ask(self) -> None:
-  """Responds with rejection for a pending /api/ask request."""
+  """
+  Responds with rejection for a pending /api/ask request.
+    [C: src/gui_2.py:App._gui_func]
+  """
   if not self._ask_request_id: return
   request_id = self._ask_request_id
 
@@ -2540,7 +2726,10 @@ class AppController:
   self._ask_tool_data = None
 
  def _handle_reset_session(self) -> None:
-  """Logic for resetting the AI session and GUI state."""
+  """
+  Logic for resetting the AI session and GUI state.
+    [C: src/gui_2.py:App._render_message_panel]
+  """
   ai_client.reset_session()
   ai_client.clear_comms_log()
   self._tool_log.clear()
@@ -2568,9 +2757,15 @@ class AppController:
    self._pending_gui_tasks.clear()
 
  def _handle_md_only(self) -> None:
-  """Logic for the 'MD Only' action."""
+  """
+  Logic for the 'MD Only' action.
+    [C: src/gui_2.py:App._render_message_panel]
+  """
 
   def worker():
+   """
+   [C: tests/test_symbol_parsing.py:test_handle_generate_send_appends_definitions, tests/test_symbol_parsing.py:test_handle_generate_send_no_symbols]
+   """
    try:
     md, path, *_ = self._do_generate()
     self.last_md = md
@@ -2583,9 +2778,15 @@ class AppController:
   threading.Thread(target=worker, daemon=True).start()
 
  def _handle_generate_send(self) -> None:
-  """Logic for the 'Gen + Send' action."""
+  """
+  Logic for the 'Gen + Send' action.
+    [C: src/gui_2.py:App._render_message_panel, src/gui_2.py:App._render_synthesis_panel, src/gui_2.py:App._render_takes_panel, tests/test_gui_events_v2.py:test_handle_generate_send_pushes_event, tests/test_symbol_parsing.py:test_handle_generate_send_appends_definitions, tests/test_symbol_parsing.py:test_handle_generate_send_no_symbols]
+  """
 
   def worker():
+   """
+   [C: tests/test_symbol_parsing.py:test_handle_generate_send_appends_definitions, tests/test_symbol_parsing.py:test_handle_generate_send_no_symbols]
+   """
    sys.stderr.write("[DEBUG] _handle_generate_send worker started\n")
    sys.stderr.flush()
    try:
@@ -2650,6 +2851,9 @@ class AppController:
   self._cached_files = stats.get("cached_files", [])
 
  def _refresh_api_metrics(self, payload: dict[str, Any], md_content: str | None = None) -> None:
+  """
+  [C: tests/test_gui_updates.py:test_telemetry_data_updates_correctly]
+  """
   if "latency" in payload:
    self.session_usage["last_latency"] = payload["latency"]
   if "usage" in payload and "percentage" in payload["usage"]:
@@ -2674,11 +2878,17 @@ class AppController:
   self._cached_tool_stats = dict(self._tool_stats)
 
  def clear_cache(self) -> None:
+  """
+  [C: src/gui_2.py:App._render_cache_panel]
+  """
   from src import ai_client
   ai_client.cleanup()
   self._update_cached_stats()
 
  def get_session_insights(self) -> Dict[str, Any]:
+  """
+  [C: src/gui_2.py:App._render_session_insights_panel]
+  """
   from src import cost_tracker
   total_input = sum(e["input"] for e in self._token_history)
   total_output = sum(e["output"] for e in self._token_history)
@@ -2701,6 +2911,9 @@ class AppController:
   }
 
  def _flush_to_project(self) -> None:
+  """
+  [C: src/gui_2.py:App._gui_func, src/gui_2.py:App._render_discussion_panel, src/gui_2.py:App._render_projects_panel, src/gui_2.py:App._show_menus]
+  """
   proj = self.project
   proj.setdefault("output", {})["output_dir"] = self.ui_output_dir
   proj.setdefault("files", {})["base_dir"] = self.ui_files_base_dir
@@ -2738,6 +2951,9 @@ class AppController:
   project_manager.save_project(cleaned_proj, self.active_project_path)
 
  def _flush_to_config(self) -> None:
+  """
+  [C: src/gui_2.py:App._gui_func, src/gui_2.py:App._render_discussion_panel, src/gui_2.py:App._render_projects_panel, src/gui_2.py:App._render_theme_panel, src/gui_2.py:App._show_menus, tests/test_system_prompt_exposure.py:TestSystemPromptExposure.test_app_controller_flush_saves_prompts]
+  """
   self.config["ai"] = {
    "provider": self.current_provider,
    "model": self.current_model,
@@ -2778,7 +2994,10 @@ class AppController:
   theme.save_to_config(self.config)
 
  def _do_generate(self) -> tuple[str, Path, list[dict[str, Any]], str, str]:
-  """Returns (full_md, output_path, file_items, stable_md, discussion_text)."""
+  """
+  Returns (full_md, output_path, file_items, stable_md, discussion_text).
+    [C: src/gui_2.py:App._show_menus, tests/test_tiered_aggregation.py:test_app_controller_do_generate_uses_persona_strategy]
+  """
   self._flush_to_project()
   self._flush_to_config()
   models.save_config(self.config)
@@ -2809,6 +3028,9 @@ class AppController:
   return full_md, path, file_items, stable_md, discussion_text
 
  def _cb_plan_epic(self) -> None:
+  """
+  [C: src/gui_2.py:App._render_mma_dashboard, tests/test_mma_orchestration_gui.py:test_cb_plan_epic_launches_thread]
+  """
   def _bg_task() -> None:
    sys.stderr.write("[DEBUG] _cb_plan_epic _bg_task started\n")
    sys.stderr.flush()
@@ -2855,6 +3077,9 @@ class AppController:
   threading.Thread(target=_bg_task, daemon=True).start()
 
  def _cb_accept_tracks(self) -> None:
+  """
+  [C: src/gui_2.py:App._render_track_proposal_modal]
+  """
   self._show_track_proposal_modal = False
 
   def _bg_task() -> None:
@@ -2896,6 +3121,9 @@ class AppController:
   threading.Thread(target=_bg_task, daemon=True).start()
 
  def _cb_start_track(self, user_data: Any = None) -> None:
+  """
+  [C: src/gui_2.py:App._render_track_proposal_modal]
+  """
   if isinstance(user_data, str):
   # If track_id is provided directly
    track_id = user_data
@@ -3005,6 +3233,9 @@ class AppController:
    print(f"ERROR in _start_track_logic: {e}")
 
  def _cb_ticket_retry(self, ticket_id: str) -> None:
+  """
+  [C: tests/test_mma_ticket_actions.py:test_cb_ticket_retry]
+  """
   for t in self.active_tickets:
    if t.get('id') == ticket_id:
     t['status'] = 'todo'
@@ -3012,6 +3243,9 @@ class AppController:
   self.event_queue.put("mma_retry", {"ticket_id": ticket_id})
 
  def _cb_ticket_skip(self, ticket_id: str) -> None:
+  """
+  [C: tests/test_mma_ticket_actions.py:test_cb_ticket_skip]
+  """
   for t in self.active_tickets:
    if t.get('id') == ticket_id:
     t['status'] = 'skipped'
@@ -3031,7 +3265,10 @@ class AppController:
   self.event_queue.put("mma_retry", {"ticket_id": ticket_id})
 
  def kill_worker(self, worker_id: str) -> None:
-  """Aborts a running worker."""
+  """
+  Aborts a running worker.
+    [C: src/gui_2.py:App._cb_kill_ticket, tests/test_conductor_engine_abort.py:test_kill_worker_sets_abort_and_joins_thread]
+  """
   engine = self.engines.get(self.active_track.id if self.active_track else None)
   if engine:
    engine.kill_worker(worker_id)
@@ -3051,7 +3288,10 @@ class AppController:
    engine.resume()
 
  def inject_context(self, data: dict) -> None:
-  """Programmatic context injection."""
+  """
+  Programmatic context injection.
+    [C: tests/test_headless_simulation.py:test_mma_track_lifecycle_simulation]
+  """
   file_path = data.get("file_path")
   if file_path:
    if not os.path.isabs(file_path):
@@ -3097,6 +3337,9 @@ class AppController:
    self._push_mma_state_update()
 
  def _cb_run_conductor_setup(self) -> None:
+  """
+  [C: src/gui_2.py:App._render_mma_dashboard, tests/test_gui_phase3.py:test_conductor_setup_scan]
+  """
   base = paths.get_conductor_dir(project_path=self.active_project_root)
   if not base.exists():
    self.ui_conductor_setup_summary = f"Error: {base}/ directory not found."
@@ -3124,6 +3367,9 @@ class AppController:
   self.ui_conductor_setup_summary = "\n".join(summary)
 
  def _cb_create_track(self, name: str, desc: str, track_type: str) -> None:
+  """
+  [C: src/gui_2.py:App._render_mma_dashboard, tests/test_gui_phase3.py:test_create_track]
+  """
   if not name: return
   date_suffix = datetime.now().strftime("%Y%m%d")
   track_id = f"{name.lower().replace(' ', '_')}_{date_suffix}"
@@ -3149,6 +3395,9 @@ class AppController:
   self.tracks = project_manager.get_all_tracks(self.active_project_root)
 
  def _push_mma_state_update(self) -> None:
+  """
+  [C: src/gui_2.py:App._cb_block_ticket, src/gui_2.py:App._cb_unblock_ticket, src/gui_2.py:App._render_mma_dashboard, src/gui_2.py:App._render_task_dag_panel, src/gui_2.py:App._render_ticket_queue, src/gui_2.py:App._reorder_ticket, src/gui_2.py:App.bulk_block, src/gui_2.py:App.bulk_execute, src/gui_2.py:App.bulk_skip, tests/test_gui_phase4.py:test_push_mma_state_update]
+  """
   if not self.active_track:
    return
    # Sync active_tickets (list of dicts) back to active_track.tickets (list of models.Ticket objects)
@@ -3170,7 +3419,10 @@ class AppController:
   project_manager.save_track_state(self.active_track.id, state, self.active_project_root)
 
  def _load_active_tickets(self) -> None:
-  """Populates self.active_tickets based on the current execution mode."""
+  """
+  Populates self.active_tickets based on the current execution mode.
+    [C: tests/test_gui_dag_beads.py:test_load_active_tickets_from_beads]
+  """
   if getattr(self, "ui_project_execution_mode", "native") == "beads":
    from src import beads_client
    bclient = beads_client.BeadsClient(Path(self.active_project_root))
@@ -3191,4 +3443,3 @@ class AppController:
     self.active_tickets = [asdict(t) if not isinstance(t, dict) else t for t in self.active_track.tickets]
    else:
     self.active_tickets = []
-