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()