Restructure/rename directories and files

[steplica]

• Rename dto/ package from Request to request
• Add sub-package to dto/ called response
• Move active site parse logic from parser to parser/activesite
• Remove WEB-INF folder because it's no longer required
• Renamed variables to follow Java conventions
• Cleaned up pom.xml
• Optimized import statements
• Correct type levenstein to levenshtein
• Cleaned up log statements to use Slf4j variable interpolation
• Removed unused PDB/mmCIF protein readers

[blackpan2]

Fixes #122

[steplica]

@blackpan2 @jmiller656 I updated, merged with dev, and tested. Can y'all check this out to make sure it looks good?