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/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"