refactor: modernize code quality tooling with Ruff

- Replace black, isort, and flake8 with Ruff (all-in-one linter and formatter)
- Add comprehensive pyproject.toml configuration
- Simplify Makefile code quality targets
- Configure exclusions for venv/.venv in pyproject.toml
- Auto-fix 1,359 linting issues across codebase

Benefits:
- Much faster builds (Ruff is written in Rust)
- Single tool replaces multiple tools
- More comprehensive rule set (UP, B, C4, SIM, PIE, RET, Q)
- All configuration centralized in pyproject.toml
- Better import sorting and formatting consistency

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

scripts/show_structure.py

@@ -15,7 +15,6 @@ import subprocess
 import sys
 from datetime import datetime
 from pathlib import Path
-from typing import Dict, List
 
 
 def count_files(directory: str, pattern: str) -> int:
@@ -38,7 +37,7 @@ def count_files(directory: str, pattern: str) -> int:
     return count
 
 
-def get_tree_structure(directory: str, exclude_patterns: List[str] = None) -> str:
+def get_tree_structure(directory: str, exclude_patterns: list[str] = None) -> str:
     """Generate tree structure for directory."""
     if not os.path.exists(directory):
         return f"Directory {directory} not found"
@@ -55,19 +54,18 @@ def get_tree_structure(directory: str, exclude_patterns: List[str] = None) -> st
                 errors="replace",
             )
             return result.stdout
-        else:
-            # Linux/Mac tree command with exclusions
-            exclude_args = []
-            if exclude_patterns:
-                exclude_args = ["-I", "|".join(exclude_patterns)]
+        # Linux/Mac tree command with exclusions
+        exclude_args = []
+        if exclude_patterns:
+            exclude_args = ["-I", "|".join(exclude_patterns)]
 
-            result = subprocess.run(
-                ["tree", "-F", "-a"] + exclude_args + [directory],
-                capture_output=True,
-                text=True,
-            )
-            if result.returncode == 0:
-                return result.stdout
+        result = subprocess.run(
+            ["tree", "-F", "-a"] + exclude_args + [directory],
+            capture_output=True,
+            text=True,
+        )
+        if result.returncode == 0:
+            return result.stdout
     except (subprocess.SubprocessError, FileNotFoundError):
         pass
 
@@ -76,7 +74,7 @@ def get_tree_structure(directory: str, exclude_patterns: List[str] = None) -> st
 
 
 def generate_manual_tree(
-    directory: str, exclude_patterns: List[str] = None, prefix: str = ""
+    directory: str, exclude_patterns: list[str] = None, prefix: str = ""
 ) -> str:
     """Generate tree structure manually when tree command is not available."""
     if exclude_patterns is None:
@@ -567,7 +565,7 @@ def generate_test_structure() -> str:
                 if file.startswith("test_") and file.endswith(".py"):
                     filepath = os.path.join(root, file)
                     try:
-                        with open(filepath, "r", encoding="utf-8") as f:
+                        with open(filepath, encoding="utf-8") as f:
                             for line in f:
                                 if line.strip().startswith("def test_"):
                                     test_function_count += 1