Cleanup

[amaslan]

Small fixes:

• bed file aggregate column naming changed to methylated and total rather than mA and A
• link to protocols.io from GitHub page
• under basecalling recommendations, add suggestion to baseball separately from the sequencing run
• update file paths for tutorial to be complete for test files
• clean up code / remove unnecessary comments
• update C to CG file naming for browser pdfs and bed files (also update example plots accordingly in documentation/demo)

[amaslan]

@thekugelmeister @reetm09 - can one of you review this PR? thank you!