Dev ClipKIT 2.0

[JLSteenwyk]

Major rehaul under-the-hood to support a browser application and API.

Changes include:

• MSA class introduced
• Python 3.9 and 3.10 are supported. Sunsetted early python version support
• Cleaned up sequence type determination
• Code quality improvements
• Improving logging quality
• Black formatter introduced
• Early exits where possible
• Reduced memory when not using complement flag