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/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")