# aggregate.py
from __future__ import annotations
"""
Note(Gemini):
This module orchestrates the construction of the final Markdown context string. 
Instead of sending every file to the AI raw (which blows up tokens), this uses a pipeline:
1. Resolve paths (handles globs and absolute paths).
2. Build file items (raw content).
3. If 'summary_only' is true (which is the default behavior now), it pipes the files through 
   summarize.py to generate a compacted view.
   
This is essential for keeping prompt tokens low while giving the AI enough structural info 
to use the MCP tools to fetch only what it needs.
"""
import tomllib
import re
import glob
import os
from pathlib import Path, PureWindowsPath
from typing import Any, cast
from src import summarize
from src import project_manager
from src import beads_client
from src.file_cache import ASTParser
from src.performance_monitor import get_monitor

def find_next_increment(output_dir: Path, namespace: str) -> int:
 pattern = re.compile(rf"^{re.escape(namespace)}_(\d+)\.md$")
 max_num = 0
 for f in output_dir.iterdir():
  if f.is_file():
   match = pattern.match(f.name)
   if match:
    max_num = max(max_num, int(match.group(1)))
 return max_num + 1

def is_absolute_with_drive(entry: str) -> bool:
 try:
  p = PureWindowsPath(entry)
  return p.drive != ""
 except Exception:
  return False

def resolve_paths(base_dir: Path, entry: str) -> list[Path]:
 has_drive = is_absolute_with_drive(entry)
 is_wildcard = "*" in entry
 matches = []
 if is_wildcard:
  root = Path(entry) if has_drive else base_dir / entry
  matches = [Path(p) for p in glob.glob(str(root), recursive=True) if Path(p).is_file()]
 else:
  p = Path(entry) if has_drive else (base_dir / entry).resolve()
  matches = [p]
  # Blacklist filter
 filtered = []
 for p in matches:
  name = p.name.lower()
  if name == "history.toml" or name.endswith("_history.toml"):
   continue
  filtered.append(p)
 return sorted(filtered)

def group_files_by_dir(files: list[Any]) -> dict[str, list[Any]]:
 """Groups FileItem objects by their relative directory path."""
 grouped = {}
 for f in files:
  path_str = f.path if hasattr(f, 'path') else str(f)
  # Normalize path separators
  path_str = path_str.replace('\\', '/')
  dir_name = os.path.dirname(path_str)
  if not dir_name:
   dir_name = "."
  if dir_name not in grouped:
   grouped[dir_name] = []
  grouped[dir_name].append(f)
 return grouped

def compute_file_stats(abs_path: str) -> dict[str, int]:
 """Computes lines and basic AST stats for a file."""
 stats = {"lines": 0, "ast_elements": 0}
 try:
  with open(abs_path, 'r', encoding='utf-8') as f:
   content = f.read()
   stats["lines"] = len(content.splitlines())
   if abs_path.endswith('.py'):
    import ast
    try:
     tree = ast.parse(content)
     stats["ast_elements"] = sum(1 for node in ast.walk(tree) if isinstance(node, (ast.FunctionDef, ast.AsyncFunctionDef, ast.ClassDef)))
    except Exception:
     pass
 except Exception:
  pass
 return stats

def build_discussion_section(history: list[Any]) -> str:
 """
 
  
      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):
   role = entry.get("role", "Unknown")
   content = entry.get("content", "").strip()
   text = f"{role}: {content}"
  else:
   text = str(entry).strip()
  sections.append(f"### Discussion Excerpt {i}\n\n{text}")
 return "\n\n---\n\n".join(sections)


def build_screenshots_section(base_dir: Path, screenshots: list[str]) -> str:
 sections = []
 for entry in screenshots:
  if not entry or not isinstance(entry, str):
   continue
  paths = resolve_paths(base_dir, entry)
  if not paths:
   sections.append(f"### `{entry}`\n\n_ERROR: no files matched: {entry}_")
   continue
  for path in paths:
   original = entry if "*" not in entry else str(path)
   if not path.exists():
    sections.append(f"### `{original}`\n\n_ERROR: file not found: {path}_")
    continue
   sections.append(f"### `{original}`\n\n![{path.name}]({path.as_posix()})")
 return "\n\n---\n\n".join(sections)

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
          view_mode      : str   (summary, full, skeleton, outline, none)
  [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]] = []
  parser = None
  for entry_raw in files:
   if isinstance(entry_raw, dict):
    entry = cast(str, entry_raw.get("path", ""))
    tier = entry_raw.get("tier")
    auto_aggregate = entry_raw.get("auto_aggregate", True)
    force_full = entry_raw.get("force_full", False)
    view_mode = entry_raw.get("view_mode", "full")
    if force_full:
     view_mode = "full"
    ast_signatures = entry_raw.get("ast_signatures", False)
    ast_definitions = entry_raw.get("ast_definitions", False)
    ast_mask = entry_raw.get("ast_mask", {})
    custom_slices = entry_raw.get("custom_slices", [])
   elif hasattr(entry_raw, "path"):
    entry = entry_raw.path
    tier = getattr(entry_raw, "tier", None)
    auto_aggregate = getattr(entry_raw, "auto_aggregate", True)
    force_full = getattr(entry_raw, "force_full", False)
    view_mode = getattr(entry_raw, "view_mode", "full")
    if force_full:
     view_mode = "full"
    ast_signatures = getattr(entry_raw, "ast_signatures", False)
    ast_definitions = getattr(entry_raw, "ast_definitions", False)
    ast_mask = getattr(entry_raw, "ast_mask", {})
    custom_slices = getattr(entry_raw, "custom_slices", [])
   else:
    entry = entry_raw
    tier = None
    auto_aggregate = True
    force_full = False
    view_mode = "full"
    ast_signatures = False
    ast_definitions = False
    ast_mask = {}
    custom_slices = []
   if not entry or not isinstance(entry, str):
    continue
   paths = resolve_paths(base_dir, entry)
   if not paths:
    items.append({"path": None, "entry": entry, "content": f"ERROR: no files matched: {entry}", "error": True, "mtime": 0.0, "tier": tier, "auto_aggregate": auto_aggregate, "force_full": force_full, "view_mode": view_mode, "ast_signatures": ast_signatures, "ast_definitions": ast_definitions, "ast_mask": ast_mask, "custom_slices": custom_slices})
    continue
   for path in paths:
    try:
     content = path.read_text(encoding="utf-8")
     mtime = path.stat().st_mtime
     error = False
     if not error and view_mode != "full":
      if view_mode == "summary":
       content = summarize.summarise_file(path, content)
      elif view_mode == "skeleton":
       if path.suffix == ".py":
        if not parser: parser = ASTParser("python")
        content = parser.get_skeleton(content, path=str(path))
       else:
        content = summarize.summarise_file(path, content)
      elif view_mode == "outline":
       if path.suffix == ".py":
        if not parser: parser = ASTParser("python")
        content = parser.get_code_outline(content, path=str(path))
       else:
        content = summarize.summarise_file(path, content)
      elif view_mode == "none":
       content = "(context excluded)"
      elif view_mode == "custom":
       if custom_slices:
        lines = content.splitlines()
        slices_text = []
        for s in custom_slices:
         start = s.get("start_line", 1)
         end = s.get("end_line", len(lines))
         tag = s.get("tag", "unnamed")
         comment = s.get("comment", "")
         s_idx = max(0, start - 1)
         e_idx = min(len(lines), end)
         chunk = "\n".join(lines[s_idx:e_idx])
         slices_text.append(f"---\n[Slice: {tag}] ({comment})\nLines {start}-{end}:\n{chunk}")
        content = "\n\n".join(slices_text)
       else:
        content = summarize.summarise_file(path, content)
    except FileNotFoundError:
     content = f"ERROR: file not found: {path}"
     mtime = 0.0
     error = True
    except Exception as e:
     content = f"ERROR: {e}"
     mtime = 0.0
     error = True
    items.append({"path": path, "entry": entry, "content": content, "error": error, "mtime": mtime, "tier": tier, "auto_aggregate": auto_aggregate, "force_full": force_full, "view_mode": view_mode, "ast_signatures": ast_signatures, "ast_definitions": ast_definitions, "ast_mask": ast_mask, "custom_slices": custom_slices})
  return 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).
  [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):
   continue
  path = item.get("path")
  entry = item.get("entry", "unknown")
  content = item.get("content", "")
  view_mode = item.get("view_mode", "full")
  if path is None:
   if view_mode == "summary":
    sections.append(f"### `{entry}`\n\n{content}")
   else:
    sections.append(f"### `{entry}`\n\n```text\n{content}\n```")
  else:
   path_obj = Path(path) if isinstance(path, str) else path
   suffix = path_obj.suffix.lstrip(".") if path_obj.suffix else "text"
   original = entry if "*" not in entry else str(path)
   if view_mode == "summary":
    sections.append(f"### `{original}`\n\n{content}")
   else:
    sections.append(f"### `{original}`\n\n```{suffix}\n{content}\n```")
 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 ""
 beads = client.list_beads()
 if not beads:
  return ""
 active = [b for b in beads if b.status == "active"]
 completed = [b for b in beads if b.status == "completed"]
 parts = []
 parts.append("## Beads Mode: Progress Track")
 if completed:
  parts.append("### Completed Beads")
  comp_list = ", ".join([f"`{b.title}`" for b in completed])
  parts.append(comp_list)
 if active:
  parts.append("### Active Beads")
  for b in active:
   parts.append(f"- **{b.title}** ({b.id}): {b.description}")
 return "\n\n".join(parts)

def build_markdown_from_items(file_items: list[dict[str, Any]], screenshot_base_dir: Path, screenshots: list[str], history: list[str], summary_only: bool = False, aggregation_strategy: str = "auto", execution_mode: str = "standard", base_dir: Path | None = None) -> str:
 """Build markdown from pre-read file items instead of re-reading from disk."""
 parts = []
 # STATIC PREFIX: Files and Screenshots must go first to maximize Cache Hits
 if file_items:
  if aggregation_strategy == "summarize":
   parts.append("## Files (Summary)\n\n" + summarize.build_summary_markdown(file_items))
  elif aggregation_strategy == "full":
   parts.append("## Files\n\n" + _build_files_section_from_items(file_items))
  else: # auto
   if summary_only:
    parts.append("## Files (Summary)\n\n" + summarize.build_summary_markdown(file_items))
   else:
    parts.append("## Files\n\n" + _build_files_section_from_items(file_items))
 if screenshots:
  parts.append("## Screenshots\n\n" + build_screenshots_section(screenshot_base_dir, screenshots))
 if execution_mode == "beads" and base_dir:
  beads_md = build_beads_section(base_dir)
  if beads_md:
   parts.append(beads_md)
 # DYNAMIC SUFFIX: History changes every turn, must go last
 if history:
  parts.append("## Discussion History\n\n" + build_discussion_section(history))
 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.
  [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.
  [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_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.
  [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")
  sections = []
  for item in file_items:
   if not item.get("auto_aggregate", True):
    continue
   path = item.get("path")
   entry = item.get("entry", "")
   path_str = str(path) if path else ""
   name = path.name if path else ""
   tier = item.get("tier")
   force_full = item.get("force_full")
   ast_signatures = item.get("ast_signatures", False)
   ast_definitions = item.get("ast_definitions", False)
   ast_mask = item.get("ast_mask", {})
   content = item.get("content", "")
   is_focus = entry in focus_set or (name and name in focus_set) or (path_str and path_str in focus_set)
   if not is_focus and path_str:
    for focus in focus_set:
     if focus in path_str:
      is_focus = True
      break
   original = entry if entry and "*" not in entry else (str(path) if path else (entry or "unknown"))
   
   slices = item.get('custom_slices', [])
   if slices and not item.get('error'):
    from src.fuzzy_anchor import FuzzyAnchor
    resolved_blocks = []
    content = item.get('content', '')
    suffix = path.suffix.lstrip(".") if path and path.suffix else "text"
    for slc in slices:
     range_res = FuzzyAnchor.resolve_slice(content, slc)
     if range_res:
      s, e = range_res
      lines = content.splitlines()
      resolved_blocks.append("\n".join(lines[s-1:e]))
    if resolved_blocks:
     combined = "\n\n... [LINES SKIPPED] ...\n\n".join(resolved_blocks)
     sections.append(f"### `{original}` (Slices)\n\n```{suffix}\n{combined}\n```")
     continue # Skip full file logic

   if is_focus or tier == 3 or force_full:
    suffix = path.suffix.lstrip(".") if path and path.suffix else "text"
    sections.append(f"### `{original}`\n\n```{suffix}\n{content}\n```")
   elif path:
    if ast_mask and not item.get("error"):
     mask_sections = []
     from src import mcp_client
     for symbol, mode in ast_mask.items():
      if mode == "hide":
       continue
      res = ""
      if path.suffix == ".py":
       res = mcp_client.py_get_definition(str(path), symbol) if mode == "def" else mcp_client.py_get_signature(str(path), symbol)
      elif path.suffix in [".c", ".h", ".cpp", ".hpp", ".cxx", ".cc"]:
       is_cpp = any(ext in path.suffix for ext in [".cpp", ".hpp", ".cxx", ".cc"])
       if mode == "def":
        res = mcp_client.ts_cpp_get_definition(str(path), symbol) if is_cpp else mcp_client.ts_c_get_definition(str(path), symbol)
       else:
        res = mcp_client.ts_cpp_get_signature(str(path), symbol) if is_cpp else mcp_client.ts_c_get_signature(str(path), symbol)
      if res:
       mask_sections.append(res)
     if mask_sections:
      suffix = path.suffix.lstrip(".") if path.suffix else "text"
      sections.append(f"### `{original}` (Masked)\n\n```{suffix}\n" + "\n\n".join(mask_sections) + "\n```")
      continue
    if path.suffix in ['.c', '.h', '.cpp', '.hpp', '.cxx', '.cc'] and not item.get("error"):
     from src import mcp_client
     if ast_definitions:
      skeleton = mcp_client.ts_cpp_get_skeleton(str(path)) if 'cpp' in path.suffix or 'hpp' in path.suffix or 'cxx' in path.suffix or 'cc' in path.suffix else mcp_client.ts_c_get_skeleton(str(path))
      sections.append(f"### `{original}` (AST Definitions)\n\n```{path.suffix.lstrip('.')}\n{skeleton}\n```")
     elif ast_signatures:
      outline = mcp_client.ts_cpp_get_code_outline(str(path)) if 'cpp' in path.suffix or 'hpp' in path.suffix or 'cxx' in path.suffix or 'cc' in path.suffix else mcp_client.ts_c_get_code_outline(str(path))
      sections.append(f"### `{original}` (AST Signatures)\n\n```{path.suffix.lstrip('.')}\n{outline}\n```")
     else:
      sections.append(f"### `{original}`\n\n{summarize.summarise_file(path, content)}")
    elif path.suffix == ".py" and not item.get("error"):
     try:
      skeleton = parser.get_skeleton(content)
      sections.append(f"### `{original}` (AST Skeleton)\n\n```python\n{skeleton}\n```")
     except Exception:
      sections.append(f"### `{original}`\n\n{summarize.summarise_file(path, content)}")
    else:
     sections.append(f"### `{original}`\n\n{summarize.summarise_file(path, content)}")
  parts = []
  if sections:
   parts.append("## Files (Tier 3 - Focused)\n\n" + "\n\n---\n\n".join(sections))
  if screenshots:
   parts.append("## Screenshots\n\n" + build_screenshots_section(screenshot_base_dir, screenshots))
  if history:
   parts.append("## Discussion History\n\n" + build_discussion_section(history))
  return "\n\n---\n\n".join(parts)

def build_markdown(base_dir: Path, files: list[str | dict[str, Any]], screenshot_base_dir: Path, screenshots: list[str], history: list[str], summary_only: bool = False, execution_mode: str = "standard") -> str:
 file_items = build_file_items(base_dir, files)
 return build_markdown_from_items(file_items, screenshot_base_dir, screenshots, history, summary_only=summary_only, aggregation_strategy='auto', execution_mode=execution_mode, base_dir=base_dir)

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")
 output_dir = Path(config["output"]["output_dir"])
 base_dir = Path(config["files"]["base_dir"])
 files = config["files"].get("paths", [])
 screenshot_base_dir = Path(config.get("screenshots", {}).get("base_dir", "."))
 screenshots = config.get("screenshots", {}).get("paths", [])
 history = config.get("discussion", {}).get("history", [])
 output_dir.mkdir(parents=True, exist_ok=True)
 increment = find_next_increment(output_dir, namespace)
 output_file = output_dir / f"{namespace}_{increment:03d}.md"
 # Build file items once, then construct markdown from them (avoids double I/O)
 file_items = build_file_items(base_dir, files)
 summary_only = config.get("project", {}).get("summary_only", False)
 execution_mode = config.get("project", {}).get("execution_mode", "standard")
 markdown = build_markdown_from_items(file_items, screenshot_base_dir, screenshots, history,
  summary_only=summary_only, aggregation_strategy=aggregation_strategy, execution_mode=execution_mode, base_dir=base_dir)
 output_file.write_text(markdown, encoding="utf-8")
 return markdown, output_file, file_items

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():

  print(f"{config_path} not found.")
  return
 with open(config_path, "rb") as f:
  global_cfg = tomllib.load(f)
 active_path = global_cfg.get("projects", {}).get("active")
 if not active_path:
  print(f"No active project found in {config_path}.")
  return
  # Use project_manager to load project (handles history segregation)
 proj = project_manager.load_project(active_path)
 # Use flat_config to make it compatible with aggregate.run()
 config = project_manager.flat_config(proj)
 markdown, output_file, _ = run(config)
 print(f"Written: {output_file}")

if __name__ == "__main__":
 main()