JSHint fixes (including indentation & whitespace);

This PR includes:
* [JSHint](http://jshint.com) warning fixes.
* Style consistency (including indentation & whitespace).

No functionality should have been changed!

Node modules & ace has been ignored.

Some files still have warnings, but those warnings needs addressing later as it mite involve functionality changes:
* `controllers/_template.js`
* `controllers/scriptStorage.js`
* `controllers/user.js`
* `libs/modelQuery.js`
* `libs/modifySessions.js`
* `libs/muExpress.js`
* `libs/remove.js`
* `libs/templateHelpers.js`

Hoping that this can reviewed asap to keep conflicts as a minimum.
Why is your indentation program removing a necessary space here?