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>

tests/test_package_structure.py

@@ -24,7 +24,7 @@ class TestCliPackage:
         import skill_seekers.cli
 
         assert hasattr(skill_seekers.cli, "__version__")
-        assert skill_seekers.cli.__version__ == "3.0.0"
+        assert skill_seekers.cli.__version__ == "3.1.0"
 
     def test_cli_has_all(self):
         """Test that skill_seekers.cli package has __all__ export list."""
@@ -88,7 +88,7 @@ class TestMcpPackage:
         import skill_seekers.mcp
 
         assert hasattr(skill_seekers.mcp, "__version__")
-        assert skill_seekers.mcp.__version__ == "3.0.0"
+        assert skill_seekers.mcp.__version__ == "3.1.0"
 
     def test_mcp_has_all(self):
         """Test that skill_seekers.mcp package has __all__ export list."""
@@ -108,7 +108,7 @@ class TestMcpPackage:
         import skill_seekers.mcp.tools
 
         assert hasattr(skill_seekers.mcp.tools, "__version__")
-        assert skill_seekers.mcp.tools.__version__ == "3.0.0"
+        assert skill_seekers.mcp.tools.__version__ == "3.1.0"
 
 
 class TestPackageStructure:
@@ -212,7 +212,7 @@ class TestRootPackage:
         import skill_seekers
 
         assert hasattr(skill_seekers, "__version__")
-        assert skill_seekers.__version__ == "3.0.0"
+        assert skill_seekers.__version__ == "3.1.0"
 
     def test_root_has_metadata(self):
         """Test that skill_seekers root package has metadata."""