chore: bump version to 3.1.0 and update CHANGELOG

- pyproject.toml: version 3.0.0 → 3.1.0
- src/skill_seekers/_version.py: update hardcoded fallback to 3.1.0
- CHANGELOG.md: comprehensive [3.1.0] release notes covering all
  features and fixes since v3.0.0 (unified create command, workflow
  presets, RST parser, smart enhance dispatcher, CLI flag parity,
  60 new workflow YAMLs, test suite improvements)
- Deprecation messages: update "removed in v3.0.0" → "v4.0.0" across
  analyze_presets.py, codebase_scraper.py, mcp/server.py
- tests/test_cli_paths.py: update version assertion to 3.1.0
- tests/test_package_structure.py: update __version__ assertions to 3.1.0
- tests/test_preset_system.py: update deprecation message version to v4.0.0

All 2267 tests passing.

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

src/skill_seekers/_version.py

@@ -28,7 +28,7 @@ def get_version() -> str:
     """
     if tomllib is None:
         # Fallback if TOML library not available
-        return "3.0.0"  # Hardcoded fallback
+        return "3.1.0"  # Hardcoded fallback
 
     try:
         # Get path to pyproject.toml (3 levels up from this file)
@@ -37,7 +37,7 @@ def get_version() -> str:
 
         if not pyproject_path.exists():
             # Fallback for installed package
-            return "3.0.0"  # Hardcoded fallback
+            return "3.1.0"  # Hardcoded fallback
 
         with open(pyproject_path, "rb") as f:
             pyproject_data = tomllib.load(f)
@@ -46,7 +46,7 @@ def get_version() -> str:
 
     except Exception:
         # Fallback if anything goes wrong
-        return "3.0.0"  # Hardcoded fallback
+        return "3.1.0"  # Hardcoded fallback
 
 
 __version__ = get_version()

src/skill_seekers/cli/codebase_scraper.py

@@ -2251,7 +2251,7 @@ def _check_deprecated_flags(args):
         print("   --preset standard       (5-10 min, core features, DEFAULT)")
         print("   --preset comprehensive  (20-60 min, all features + AI)")
         print("   --enhance-level 0-3     (granular AI enhancement control)")
-        print("\n⚠️  Deprecated flags will be removed in v3.0.0")
+        print("\n⚠️  Deprecated flags will be removed in v4.0.0")
         print("=" * 70 + "\n")
 
 

src/skill_seekers/cli/presets/analyze_presets.py

@@ -254,6 +254,6 @@ def print_deprecation_warning(old_flag: str, new_flag: str) -> None:
         old_flag: The old/deprecated flag name
         new_flag: The new recommended flag/preset
     """
-    print(f"\n⚠️  DEPRECATED: {old_flag} is deprecated and will be removed in v3.0.0")
+    print(f"\n⚠️  DEPRECATED: {old_flag} is deprecated and will be removed in v4.0.0")
     print(f"   Use: {new_flag}")
     print()

src/skill_seekers/mcp/server.py

@@ -15,7 +15,7 @@ import warnings
 
 # Show deprecation warning (can be disabled with PYTHONWARNINGS=ignore)
 warnings.warn(
-    "The legacy server.py is deprecated and will be removed in v3.0.0. "
+    "The legacy server.py is deprecated and will be removed in v4.0.0. "
     "Please update your MCP configuration to use 'server_fastmcp' instead:\n"
     "  OLD: python -m skill_seekers.mcp.server\n"
     "  NEW: python -m skill_seekers.mcp.server_fastmcp\n"