Docs/improve comprehensive documentation

.github/workflows/auto-label.yml

@@ -4,7 +4,7 @@ name: Auto-label Bot
 on:
   issues:
     types: [opened, edited]
-  pull_request:
+  pull_request_target:
     types: [opened, edited, synchronize]
 
 permissions:
@@ -116,7 +116,7 @@ jobs:
             }
 
   label-pull-requests:
-    if: github.event_name == 'pull_request'
+    if: github.event_name == 'pull_request_target'
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code

.github/workflows/coverage.yml

@@ -3,7 +3,7 @@ name: Coverage
 on:
   push:
     branches: [ main ]
-  pull_request:
+  pull_request_target:
     branches: [ main ]
 
 jobs:
@@ -43,7 +43,7 @@ jobs:
         path: htmlcov/
 
     - name: Comment coverage on PR
-      if: github.event_name == 'pull_request'
+      if: github.event_name == 'pull_request_target'
       uses: py-cov-action/python-coverage-comment-action@v3
       with:
         GITHUB_TOKEN: ${{ github.token }}

docs/api-reference/overview.mdx

@@ -260,6 +260,71 @@ print(f"AST cache hits: {stats['ast_cache']['hits']}")
 refactron.clear_caches()
 ```
 
+## Core Modules API
+
+Refactron provides dedicated APIs for its core subsystems:
+
+### Analyzers API
+```python
+from refactron.analyzers import CodeSmellAnalyzer, SecurityAnalyzer
+
+# Run specific analyzers programmatically
+code_analyzer = CodeSmellAnalyzer(config)
+issues = code_analyzer.analyze(file_path="src/main.py")
+
+security = SecurityAnalyzer(config)
+vulns = security.detect_vulnerabilities(ast_tree)
+```
+
+### Autofix API
+```python
+from refactron.autofix import AutofixEngine
+
+engine = AutofixEngine(config)
+# Apply fixes for specified issues
+result = engine.apply_fixes(issues, backup=True)
+print(f"Fixed {result.fixed_count} issues. Backup at {result.backup_path}")
+```
+
+### LLM Integration API
+```python
+from refactron.llm import LLMProvider, PromptManager
+
+llm = LLMProvider.get_default(config)
+# Generate a documentation string
+docstring = llm.generate("Write a comprehensive Python docstring for this function", context=func_code)
+
+manager = PromptManager()
+formatted_prompt = manager.create_prompt(task_type="refactor", code_snippet=snippet)
+```
+
+### RAG API
+```python
+from refactron.rag import RAGSearch
+
+# Initialize search index
+search = RAGSearch(config)
+search.index_directory("myproject/")
+
+# Query codebase
+results = search.query("authentication logic", top_k=5)
+for res in results:
+    print(f"Match in {res.file}: {res.score}")
+```
+
+### Refactorers API
+```python
+from refactron.refactorers import ExtractConstantRefactorer
+
+refactorer = ExtractConstantRefactorer(config)
+# Check applicability
+can_refactor = refactorer.is_applicable(node)
+
+if can_refactor:
+    changes = refactorer.compute_diff(node)
+    refactorer.apply(changes)
+```
+
 ## Next Steps
 
 <Card

docs/cli/commands.mdx

@@ -265,11 +265,15 @@ refactron auth <command>
 ```
 
 **Commands:**
+- `login` - Log in to account
 - `status` - Check authentication status
 - `logout` - Log out from account
 
 **Examples:**
 ```bash
+# Login
+refactron auth login
+
 # Check auth status
 refactron auth status
 
@@ -288,16 +292,20 @@ refactron repo <command> [options]
 ```
 
 **Commands:**
+- `init` - Initialize repository
 - `list` - List connected repositories
 - `connect` - Connect a repository
 - `disconnect` - Disconnect a repository
 
 **Options:**
-- `--path PATH` - Repository path (for connect)
+- `--path PATH` - Repository path (for connect/init)
 - `--delete-files` - Delete local files (for disconnect)
 
 **Examples:**
 ```bash
+# Initialize repo
+refactron repo init
+
 # List repos
 refactron repo list
 

docs/essentials/configuration.mdx

@@ -109,33 +109,57 @@ pattern_storage_dir: null  # null = auto-detect
   </Accordion>
 </AccordionGroup>
 
-## Threshold Configuration
+## Advanced Threshold Configuration
 
-Adjust thresholds to match your project's standards:
+Refactron allows granular control over thresholds to match your team's specific coding standards. You can configure rules per-analyzer:
 
 ```yaml .refactron.yaml
-# Complexity thresholds
-max_function_complexity: 15        # Default: 10
-max_function_length: 100           # Default: 50
-max_parameters: 7                  # Default: 5
-max_nesting_depth: 4              # Default: 3
-
-# Code quality thresholds
-min_maintainability_index: 60     # Default: 65
-max_cognitive_complexity: 20      # Default: 15
+# Complexity analyzers
+complexity:
+  max_function_complexity: 15        # Default: 10
+  max_function_length: 100           # Default: 50
+  max_cognitive_complexity: 20       # Default: 15
+  min_maintainability_index: 60      # Default: 65
+
+# Code smell analyzers
+code_smell:
+  max_parameters: 7                  # Default: 5
+  max_nesting_depth: 4               # Default: 3
+  max_returns_count: 5               # Default: 3
+  max_boolean_arguments: 2           # Default: 2
+
+# Security analyzers
+security:
+  strict_mode: true                  # Fail on any security issue
+  check_subprocesses: true
+  check_sql_injection: true
 ```
 
-## Exclude Patterns
+## Advanced Exclude Patterns
 
-Exclude files or directories from analysis:
+You can define powerful exclusion rules using glob patterns, or exclude specific rules within specific directories:
 
 ```yaml .refactron.yaml
 exclude_patterns:
+  # Standard ignore patterns
   - "*/tests/*"
   - "*/migrations/*"
   - "*/venv/*"
   - "*.pyc"
   - "__pycache__"
+  # Ignore generated files
+  - "*/generated/*"
+  - "*_pb2.py"
+
+# Rule-specific exclusions
+per_file_ignores:
+  # Ignore magic numbers in test files
+  "*/tests/*":
+    - magic-number
+  # Ignore high complexity in specific legacy files
+  "legacy_module.py":
+    - complexity
+    - long-function
 ```
 
 ## Environment Variables

docs/guides/code-analysis.mdx

@@ -285,6 +285,38 @@ refactron analyze src/module1/
 refactron analyze src/module2/
 ```
 
+## Real-World Recipes
+
+### Recipe: Scanning for SQL Injection in CI
+
+A common requirement is to block pull requests that introduce critical security issues like SQL Injection. You can run Refactron in a strict mode during your CI pipeline:
+
+```yaml .github/workflows/security-scan.yml
+name: Security Scan
+on: [push, pull_request]
+
+jobs:
+  analyze:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install Refactron
+        run: pip install refactron
+      - name: Run Security Analysis
+        run: |
+          # Use focused config for CI
+          refactron analyze . \
+            --config .refactron-ci.yaml \
+            --format json -o security-report.json
+      - name: Fail on Critical Issues
+        run: |
+          # Exit with error if any critical SQLi found
+          if grep -q '"level": "CRITICAL"' security-report.json; then
+            echo "Security check failed!"
+            exit 1
+          fi
+```
+
 ## Next Steps
 
 <CardGroup cols={2}>

docs/guides/refactoring.mdx

@@ -317,6 +317,37 @@ refactron feedback <operation-id> --action accepted
   </Accordion>
 </AccordionGroup>
 
+## Real-World Recipes
+
+### Recipe: Applying Batch Refactoring
+
+When performing large-scale migrations, such as updating a legacy codebase or standardizing docstrings across hundreds of files, you can use Refactron's batch processing for automated refactoring:
+
+```python
+from refactron import Refactron
+import glob
+
+refactron = Refactron()
+
+# Get all target files
+python_files = glob.glob("legacy_app/**/*.py", recursive=True)
+
+# Apply specific refactoring type in a batch
+results = []
+for file_path in python_files:
+    # Adding docstrings to all functions
+    result = refactron.refactor(
+        file_path, 
+        preview=False, 
+        operation_types=["add_docstring", "extract_constant"],
+        risk_level="safe" # Ensure only completely safe changes apply
+    )
+    if result.success:
+        results.append(result)
+
+print(f"Successfully processed {len(results)} files automatically.")
+```
+
 ## Next Steps
 
 <CardGroup cols={2}>

pyproject.toml

@@ -80,10 +80,12 @@ profile = "black"
 line_length = 100
 
 [tool.mypy]
-python_version = "3.8"
+python_version = "3.9"
 warn_return_any = true
 warn_unused_configs = true
 disallow_untyped_defs = true
+ignore_missing_imports = true
+follow_imports = "skip"
 
 [[tool.mypy.overrides]]
 module = "tests.*"