refactor(goal): code analysis engine

changes:
  - file: cli.py
    area: cli
    removed: [_merge_chunked_results, _run_chunked_analysis, _run_streaming_analysis, _analyze_subproject, _run_analysis, on_progress]
  - file: cli_analysis.py
    area: analyzer
    added: [_merge_chunked_results, _run_chunked_analysis, _build_config, _run_streaming_analysis, _run_standard_analysis, _analyze_all_subprojects, +6 more]
  - file: cli_exports.py
    area: cli
    removed: [_export_prompt_txt, _export_project_yaml, _export_chunked_results, _export_readme, _export_simple_formats, _run_exports, +24 more]
  - file: code2logic.py
    area: cli
    added: [_build_code2logic_cmd, _find_code2logic_output, _handle_code2logic_error, _normalize_code2logic_output, _check_code2logic_installed, _run_code2logic, +2 more]
  - file: formats.py
    area: cli
    added: [_export_project_yaml, _export_readme, _export_simple_formats, _run_report, _export_evolution, _export_refactor_prompts, +4 more]
  - file: orchestrator.py
    area: cli
    added: [_export_chunked_results, _export_single_project, _run_exports]
  - file: prompt.py
    area: cli
    added: [_export_prompt_txt, _get_prompt_paths, _build_subprojects_section, _build_missing_files_section, _get_missing_files, _export_chunked_prompt_txt, +3 more]
  - file: project_yaml_exporter.py
    area: core
    added: [_group_by_file, _compute_module_entry, _build_class_export, _compute_inbound_deps, _build_function_exports]
    modified: [_build_modules, _build_exports, ProjectYAMLExporter]
  - file: validate_project.py
    area: core
    added: [validate_project_yaml, _cross_check_toon, _check_required_keys]
  - file: test_prompt_txt.py
    area: test
    modified: [test_export_code2logic_does_not_add_quiet_flag_when_verbose, test_export_code2logic_adds_quiet_flag_when_not_verbose, TestCode2logicExport]

dependencies:
  flow: "cli→cli_analysis→cli_exports, orchestrator→code2logic"
  - cli.py -> cli_exports.py
  - cli.py -> cli_analysis.py
  - cli_analysis.py -> cli_exports.py
  - orchestrator.py -> formats.py
  - orchestrator.py -> code2logic.py

stats:
  lines: "+4032/-1831 (net +2201)"
  files: 14
  complexity: "+98% complexity (monitor)"

Author: tom-sapletta-com

CHANGELOG.md

@@ -1,3 +1,35 @@
+## [0.5.38] - 2026-03-05
+
+### Summary
+
+refactor(goal): code analysis engine
+
+### Docs
+
+- docs: update README
+- docs: update context.md
+- docs: update README
+- docs: update context.md
+
+### Test
+
+- update tests/test_prompt_txt.py
+
+### Other
+
+- update analysis.toon
+- update batch_1/analysis.toon
+- update code2llm/cli.py
+- update code2llm/cli_analysis.py
+- update code2llm/cli_exports.py
+- update code2llm/cli_exports/__init__.py
+- update code2llm/cli_exports/code2logic.py
+- update code2llm/cli_exports/formats.py
+- update code2llm/cli_exports/orchestrator.py
+- update code2llm/cli_exports/prompt.py
+- ... and 6 more
+
+
 ## [0.5.37] - 2026-03-05
 
 ### Summary

README.md

@@ -10,7 +10,7 @@ When you run `code2llm ./ -f all`, the following files are created:
 
 | File | Format | Purpose | Key Insights |
 |------|--------|---------|--------------|
-| `analysis.toon` | **TOON** | **🔥 Health diagnostics** - Complexity, god modules, coupling | 55 critical functions, 1 god modules |
+| `analysis.toon` | **TOON** | **🔥 Health diagnostics** - Complexity, god modules, coupling | 52 critical functions, 0 god modules |
 | `project.toon` | **TOON** | **🧠 Project logic** - Compact module view from code2logic | Generated via code2logic integration |
 
 ### 🤖 LLM-Ready Documentation
@@ -325,9 +325,9 @@ code2llm ./ -f yaml --separate-orphans
 
 **Generated by**: `code2llm ./ -f all --readme`  
 **Analysis Date**: 2026-03-05  
-**Total Functions**: 774  
+**Total Functions**: 820  
 **Total Classes**: 104  
-**Modules**: 92  
+**Modules**: 102  
 
 For more information about code2llm, visit: https://github.com/tom-sapletta/code2llm
 

VERSION

@@ -1 +1 @@
-0.5.37
+0.5.38

analysis.toon

@@ -8,7 +8,7 @@
 and entity resolution with multilingual support.
 """
 
-__version__ = "0.5.37"
+__version__ = "0.5.38"
 __author__ = "STTS Project"
 
 # Core analysis components (lightweight, always needed)

batch_1/analysis.toon

@@ -18,6 +18,7 @@
     _export_simple_formats, _export_yaml, _export_mermaid, _export_refactor_prompts,
     _export_project_yaml, _run_report,
 )
+from .cli_analysis import _run_analysis
 
 
 
@@ -459,247 +460,7 @@ def main():
     return 0
 
 
-def _run_analysis(args, source_path: Path, output_dir: Path):
-    """Run code analysis with configured strategy.
-
-    Returns AnalysisResult or exits on error.
-    For large repos, may analyze in chunks and merge results.
-    """
-    from .core.large_repo import (
-        HierarchicalRepoSplitter, should_use_chunking, get_analysis_plan
-    )
-    
-    # Check if we should use chunked analysis
-    # Auto-chunk when estimated output > chunk_size (default 256KB = ~85 files)
-    # --no-chunk explicitly disables chunking
-    use_chunking = (
-        not args.no_chunk and
-        (args.chunk or should_use_chunking(source_path, args.chunk_size))
-    )
-    
-    if use_chunking:
-        if args.verbose:
-            print(f"Large repository detected - using chunked analysis")
-        # Set chunk flag so export knows to use chunked mode
-        args.chunk = True
-        return _run_chunked_analysis(args, source_path, output_dir)
-    
-    # Standard single-analysis flow
-    config = Config(
-        mode=args.mode,
-        max_depth_enumeration=args.max_depth,
-        detect_state_machines=not args.no_patterns,
-        detect_recursion=not args.no_patterns,
-        output_dir=str(output_dir)
-    )
-
-    try:
-        if args.streaming or args.strategy in ['quick', 'deep']:
-            result = _run_streaming_analysis(args, config, source_path)
-        else:
-            analyzer = ProjectAnalyzer(config)
-            result = analyzer.analyze_project(str(source_path))
-
-        if args.verbose:
-            print(f"\nAnalysis complete:")
-            print(f"  - Functions: {len(result.functions)}")
-            print(f"  - Classes: {len(result.classes)}")
-            print(f"  - CFG nodes: {len(result.nodes)}")
-            print(f"  - CFG edges: {len(result.edges)}")
-
-        return result
-
-    except Exception as e:
-        print(f"Error during analysis: {e}", file=sys.stderr)
-        sys.exit(1)
-
-
-def _run_chunked_analysis(args, source_path: Path, output_dir: Path):
-    """Analyze large repository using hierarchical chunking.
-    
-    Strategy:
-    1. Level 1 folders first
-    2. If >256KB, split to level 2 subfolders
-    3. If still too big, use file chunking
-    """
-    from .core.large_repo import HierarchicalRepoSplitter
-    
-    splitter = HierarchicalRepoSplitter(
-        size_limit_kb=args.chunk_size,
-        max_files_per_chunk=args.max_files_per_chunk
-    )
-    
-    # Get hierarchical analysis plan
-    subprojects = splitter.get_analysis_plan(source_path)
-    
-    if args.verbose:
-        print(f"Hierarchical analysis plan ({len(subprojects)} chunks):")
-        level_counts = {}
-        for sp in subprojects:
-            level_counts[sp.level] = level_counts.get(sp.level, 0) + 1
-        
-        for level in sorted(level_counts.keys()):
-            level_name = {0: 'root', 1: 'level-1', 2: 'level-2', 3: 'file-chunks'}.get(level, f'level-{level}')
-            print(f"  {level_name}: {level_counts[level]} chunks")
-        
-        print("\nChunks:")
-        for sp in subprojects:
-            level_indicator = "  " * sp.level
-            size_info = f"~{sp.estimated_size_kb}KB"
-            print(f"{level_indicator}{sp.name}: {sp.file_count} files ({size_info})")
-    
-    # Filter subprojects if requested
-    if args.only_subproject:
-        subprojects = [sp for sp in subprojects if sp.name == args.only_subproject or sp.name.startswith(args.only_subproject + '.')]
-        if not subprojects:
-            print(f"Error: Subproject '{args.only_subproject}' not found", file=sys.stderr)
-            sys.exit(1)
-    
-    if args.skip_subprojects:
-        subprojects = [sp for sp in subprojects if not any(sp.name.startswith(skip) for skip in args.skip_subprojects)]
-    
-    # Analyze each subproject
-    all_results = []
-    for i, subproject in enumerate(subprojects, 1):
-        if args.verbose:
-            level_name = {0: 'root', 1: 'L1', 2: 'L2', 3: 'chunk'}.get(subproject.level, f'L{subproject.level}')
-            print(f"\n[{i}/{len(subprojects)}] Analyzing [{level_name}]: {subproject.name}")
-        
-        sp_output_dir = output_dir / subproject.name.replace('.', '_')
-        sp_output_dir.mkdir(parents=True, exist_ok=True)
-        
-        result = _analyze_subproject(args, subproject, sp_output_dir)
-        if result:
-            all_results.append((subproject.name, result, sp_output_dir))
-    
-    # Create merged summary
-    merged_result = _merge_chunked_results(all_results, source_path)
-    
-    if args.verbose:
-        print(f"\nChunked analysis complete:")
-        print(f"  - Chunks analyzed: {len(all_results)}")
-        print(f"  - Total functions: {len(merged_result.functions)}")
-        print(f"  - Total classes: {len(merged_result.classes)}")
-    
-    return merged_result
-
-
-def _analyze_subproject(args, subproject, output_dir: Path):
-    """Analyze and export a single subproject."""
-    from .core.analyzer import ProjectAnalyzer
-    from .core.config import Config
-    from .cli_exports import _export_simple_formats, _export_evolution, _export_chunked_prompt_txt, _export_code2logic
-    
-    config = Config(
-        mode=args.mode,
-        max_depth_enumeration=args.max_depth,
-        detect_state_machines=not args.no_patterns,
-        detect_recursion=not args.no_patterns,
-        output_dir=str(output_dir),
-        verbose=args.verbose
-    )
-    
-    analyzer = ProjectAnalyzer(config)
-    
-    try:
-        # Analyze subproject
-        result = analyzer.analyze_project(str(subproject.path))
-        
-        # Export results for this subproject
-        formats = [f.strip() for f in args.format.split(',')]
-        if 'all' in formats:
-            formats = ['toon', 'context', 'evolution', 'code2logic']
-        
-        # Export simple formats (toon, context)
-        _export_simple_formats(args, result, output_dir, formats)
-        
-        # Export evolution
-        if 'evolution' in formats or 'all' in formats:
-            _export_evolution(args, result, output_dir)
-        
-        if args.verbose:
-            print(f"    ✓ Exported {subproject.name}: {len(result.functions)} functions")
-        
-        return result
-    except Exception as e:
-        print(f"Warning: Failed to analyze {subproject.name}: {e}", file=sys.stderr)
-        return None
-
-
-def _merge_chunked_results(all_results, source_path: Path):
-    """Merge results from multiple subproject analyses."""
-    from .core.models import AnalysisResult
-    
-    merged = AnalysisResult(project_path=str(source_path))
-    
-    for name, result, output_dir in all_results:
-        if not result:
-            continue
-        
-        # Prefix with subproject name to avoid collisions
-        prefix = f"{name}."
-        
-        # Merge functions
-        for func_name, func_info in result.functions.items():
-            new_name = f"{prefix}{func_name}" if '.' not in func_name else func_name
-            merged.functions[new_name] = func_info
-        
-        # Merge classes
-        for class_name, class_info in result.classes.items():
-            new_name = f"{prefix}{class_name}" if '.' not in class_name else class_name
-            merged.classes[new_name] = class_info
-        
-        # Merge modules
-        for mod_name, mod_info in result.modules.items():
-            new_name = f"{prefix}{mod_name}" if '.' not in mod_name else mod_name
-            merged.modules[new_name] = mod_info
-        
-        # Merge nodes and edges (simplified - just count)
-        merged.nodes.update(result.nodes)
-        merged.edges.extend(result.edges)
-    
-    return merged
-
-
-def _run_streaming_analysis(args, config, source_path: Path):
-    """Run streaming analysis with progress reporting."""
-    from .core.streaming_analyzer import (
-        StreamingAnalyzer, STRATEGY_QUICK,
-        STRATEGY_STANDARD, STRATEGY_DEEP
-    )
-
-    strategy_map = {
-        'quick': STRATEGY_QUICK,
-        'standard': STRATEGY_STANDARD,
-        'deep': STRATEGY_DEEP
-    }
-    strategy = strategy_map.get(args.strategy, STRATEGY_STANDARD)
-
-    # Adjust strategy for memory limit
-    strategy.max_files_in_memory = min(
-        strategy.max_files_in_memory,
-        args.max_memory // 10
-    )
-
-    analyzer = StreamingAnalyzer(config, strategy)
-
-    if args.verbose:
-        def on_progress(update):
-            pct = update.get('percentage', 0)
-            print(f"\r[{pct:.0f}%] {update.get('message', '')}", end='', flush=True)
-        analyzer.set_progress_callback(on_progress)
-
-    print(f"Analyzing with {args.strategy} strategy...")
-    for update in analyzer.analyze_streaming(str(source_path)):
-        if update['type'] == 'complete':
-            if args.verbose:
-                print()
-            print(f"Completed in {update.get('elapsed_seconds', 0):.1f}s")
-
-    # Re-run standard analyzer for full results
-    # TODO: Modify streaming to accumulate results properly
-    analyzer = ProjectAnalyzer(config)
-    return analyzer.analyze_project(str(source_path))
+# Analysis functions are in cli_analysis.py — imported at top of file
 
 
 def generate_llm_context(args_list):