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>

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "skill-seekers"
-version = "3.0.0"
+version = "3.1.0"
 description = "Convert documentation websites, GitHub repositories, and PDFs into Claude AI skills. International support with Chinese (简体中文) documentation."
 readme = "README.md"
 requires-python = ">=3.10"