code cleanup and add helpful comments where needed

[Maximous Black]

I would suggest that every code block (at least the ones which are fundamental to the project) should be properly commented with what it does and if there is a fix needed for a broken function and also mark the functions which cause the reported bugs so that it is easy for a new developer to help understand the code and help with the problem if they have a potential fix. I think I could have helped better with the redesign in #97 if the code was cleaner and well labeled.

I think @JoshWillik did a good job at cleaning up the code but went too far and made a major amount of change in it and that made it hard to review even if it fixed many issues (#6, #27, #31, #33, #34). So a code cleanup is required without adding or changing any functionality. we don't want what happened to #44 do we?