fix(CODEWIKI-004): CU-86akhf8u6 6 review findings across 6 files

codewiki/cli/config_manager.py

@@ -1,5 +1,16 @@
 """
 Configuration manager with keyring integration for secure credential storage.
+
+Responsibilities:
+  - Load and save non-sensitive CLI configuration (models, base URLs, API
+    versions, max tokens, temperature settings) to ~/.codewiki/config.json
+  - Store and retrieve per-role (cluster/main/fallback) API keys exclusively
+    through the system keyring, never persisting them to disk
+  - Validate configuration completeness before allowing pipeline execution
+  - Provide clear/delete operations that remove both file and keyring state
+
+This module is the single integration point between the CLI's config
+commands and the underlying Configuration dataclass and system keyring.
 """
 
 import json

codewiki/cli/utils/logging.py

@@ -1,5 +1,10 @@
 """
 Logging utilities for CLI with colored output and progress tracking.
+
+Provides CLILogger, a lightweight click-based logger with debug/info/success/
+warning/error/step helpers for user-facing CLI output, plus
+quiet_third_party_loggers(), which caps noisy third-party HTTP/SDK loggers
+(httpx, openai, anthropic) at WARNING so CLI runs stay readable.
 """
 
 import logging

codewiki/src/be/agent_tools/read_code_components.py

@@ -1,4 +1,12 @@
-"""Agent tool for reading the source code of specific CodeWiki components by id."""
+"""Agent tool for reading the source code of specific CodeWiki components by id.
+
+This module exposes `read_code_components_tool`, a pydantic-ai Tool that the
+documentation-generation agent calls to fetch the verbatim source code of one
+or more components by their fully-qualified component id (module.path::Name).
+It looks up components from the shared `CodeWikiDeps.components` map built
+earlier in the pipeline and is used by the agent to ground its explanations
+in actual source rather than hallucinated code.
+"""
 
 from pydantic_ai import RunContext, Tool
 from codewiki.src.be.agent_tools.deps import CodeWikiDeps

codewiki/src/be/dependency_analyzer/models/analysis.py

@@ -1,3 +1,13 @@
+"""
+Analysis result models for the dependency analyzer.
+
+Defines the Pydantic models used to represent the outcome of analyzing a
+repository (functions, call relationships, file tree, and summary data) as
+well as the NodeSelection model used for partial export of selected nodes.
+These models are the primary data contract passed from the dependency
+analysis stage to downstream documentation-generation and export stages.
+"""
+
 from pydantic import BaseModel
 from typing import List, Dict, Any, Optional
 from codewiki.src.be.dependency_analyzer.models.core import Node, CallRelationship, Repository

codewiki/src/be/utils.py

@@ -1,3 +1,13 @@
+"""Backend utility helpers for the CodeWiki documentation pipeline.
+
+Responsibilities:
+- Complexity heuristics for module clustering (is_complex_module)
+- Token counting via tiktoken for LLM context budgeting
+- Extraction, validation, and persistence of Mermaid diagrams embedded in
+  generated markdown documentation, including error-window rendering for
+  diagnosing parser failures.
+"""
+
 import re
 from pathlib import Path
 from typing import List, Tuple
@@ -402,4 +412,4 @@ def create_diagrams_readme(diagrams_dir: str, diagram_files: list) -> str:
     import asyncio
     test_file = "output/docs/SWE_agent-docs/agent_hooks.md"
     result = asyncio.run(validate_mermaid_diagrams(test_file, "agent_hooks.md"))
-    print(result)
+    print(result)

codewiki/src/fe/cache_manager.py

@@ -1,6 +1,13 @@
 #!/usr/bin/env python3
 """
 Cache management for documentation generation results.
+
+This module maintains an on-disk index (cache_index.json) mapping repository
+URLs to previously generated documentation output paths. It is used by the
+web-app layer (codewiki/src/fe) to avoid regenerating documentation for a
+repository that was already processed within the configured expiry window,
+including cache lookup, insertion, expiry cleanup, and recovery from a
+corrupted index file.
 """
 
 import hashlib
@@ -126,3 +133,4 @@ def cleanup_expired_cache(self):
 
         if expired_entries:
             self.save_cache_index()
+