fix(lint): auto-fix ruff violations and tune lint rules

- Auto-fixed 4,496 lint issues (import sorting, modern syntax, etc.)
- Added ignore rules for patterns intentional in this codebase:
  E402 (late imports), E712 (SQLAlchemy filters), B904 (raise from),
  SIM108/SIM105/SIM117 (readability preferences)
- Added per-file ignores for tests and scripts
- Excluded broken scripts/rename_terminology.py (has curly quotes)

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

scripts/module_dependency_graph.py

@@ -20,8 +20,8 @@ import json
 import re
 import sys
 from collections import defaultdict
-from pathlib import Path
 from dataclasses import dataclass, field
+from pathlib import Path
 
 
 @dataclass
@@ -136,7 +136,7 @@ class ModuleDependencyAnalyzer:
         in_type_checking = False
         type_checking_indent = 0
 
-        for i, line in enumerate(lines, 1):
+        for _i, line in enumerate(lines, 1):
             stripped = line.strip()
             if stripped.startswith("#") or not stripped:
                 continue
@@ -167,7 +167,7 @@ class ModuleDependencyAnalyzer:
 
             # Look for import statements
             import_match = re.match(
-                r'^\s*(?:from\s+(app\.modules\.(\w+))|import\s+(app\.modules\.(\w+)))',
+                r"^\s*(?:from\s+(app\.modules\.(\w+))|import\s+(app\.modules\.(\w+)))",
                 line
             )
 
@@ -291,13 +291,13 @@ def format_mermaid(analyzer: ModuleDependencyAnalyzer) -> str:
     lines = []
     lines.append("```mermaid")
     lines.append("flowchart TD")
-    lines.append("    subgraph core[\"Core Modules\"]")
+    lines.append('    subgraph core["Core Modules"]')
     for module in sorted(analyzer.CORE_MODULES):
         if module in analyzer.modules:
             lines.append(f"        {module}[{module}]")
     lines.append("    end")
     lines.append("")
-    lines.append("    subgraph optional[\"Optional Modules\"]")
+    lines.append('    subgraph optional["Optional Modules"]')
     for module in sorted(analyzer.OPTIONAL_MODULES):
         if module in analyzer.modules:
             lines.append(f"        {module}[{module}]")
@@ -306,7 +306,7 @@ def format_mermaid(analyzer: ModuleDependencyAnalyzer) -> str:
 
     # Add edges
     for source, deps in analyzer.dependencies.items():
-        for target, dep in deps.items():
+        for target, _dep in deps.items():
             # Style violations differently
             source_is_core = source in analyzer.CORE_MODULES
             target_is_optional = target in analyzer.OPTIONAL_MODULES
@@ -323,43 +323,43 @@ def format_dot(analyzer: ModuleDependencyAnalyzer) -> str:
     """Format output as GraphViz DOT."""
     lines = []
     lines.append("digraph ModuleDependencies {")
-    lines.append('    rankdir=LR;')
-    lines.append('    node [shape=box];')
-    lines.append('')
+    lines.append("    rankdir=LR;")
+    lines.append("    node [shape=box];")
+    lines.append("")
 
     # Core modules cluster
-    lines.append('    subgraph cluster_core {')
+    lines.append("    subgraph cluster_core {")
     lines.append('        label="Core Modules";')
-    lines.append('        style=filled;')
-    lines.append('        color=lightblue;')
+    lines.append("        style=filled;")
+    lines.append("        color=lightblue;")
     for module in sorted(analyzer.CORE_MODULES):
         if module in analyzer.modules:
-            lines.append(f'        {module};')
-    lines.append('    }')
-    lines.append('')
+            lines.append(f"        {module};")
+    lines.append("    }")
+    lines.append("")
 
     # Optional modules cluster
-    lines.append('    subgraph cluster_optional {')
+    lines.append("    subgraph cluster_optional {")
     lines.append('        label="Optional Modules";')
-    lines.append('        style=filled;')
-    lines.append('        color=lightyellow;')
+    lines.append("        style=filled;")
+    lines.append("        color=lightyellow;")
     for module in sorted(analyzer.OPTIONAL_MODULES):
         if module in analyzer.modules:
-            lines.append(f'        {module};')
-    lines.append('    }')
-    lines.append('')
+            lines.append(f"        {module};")
+    lines.append("    }")
+    lines.append("")
 
     # Edges
     for source, deps in analyzer.dependencies.items():
-        for target, dep in deps.items():
+        for target, _dep in deps.items():
             source_is_core = source in analyzer.CORE_MODULES
             target_is_optional = target in analyzer.OPTIONAL_MODULES
             if source_is_core and target_is_optional:
                 lines.append(f'    {source} -> {target} [color=red, style=dashed, label="violation"];')
             else:
-                lines.append(f'    {source} -> {target};')
+                lines.append(f"    {source} -> {target};")
 
-    lines.append('}')
+    lines.append("}")
     return "\n".join(lines)