Scan code for TODO and ensure that nothing really stupid is still in the code

[autonomous1]

I went through the list of todos and removed completed or extraneous todo comments. There were two todo's I would like to comment on:

• when generating a series of physicals from the workbench, a better naming convention is needed to ensure uniqueness otherwise the next time physicals are generated from the same virtual it will result in duplicate names. #115

• there was a question in one of the todos as to why the global variable BIONET was defined instead of 'app'. The purpose is to use a global name with a higher probability of uniqueness to avoid possible naming collisions with other packages, as well as for clarity in the code as to what package is being used. This is a common practice with packages such as PIXI or riot.

[Juul]

Alright I can look at the naming issue. We should never use packages that pollute the global namespace in any way that we don't control. If a package does this then it is a horrible piece of code that has no place in the bionet.