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Is there a way for Construct 2 to produce javascript that isn't jumbled (where it is easy to read and decipher)? Also, is there a way for Construct 2 to produce comments directly into the javascript?
Nope
For "unjembled" code, don't check the "Minify" export option and you should have plain JS code.
As for your second question could you give more informations on what is it exactly you're trying to achieve ?
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even if minify is not activated, the code is still awful to read and uncommented.
There's probably not much Scirra could do about that however as (I think) from the start it was never the intention for the exported code to be readable or editable.