Revise Fragment system
When fragments overlap, it becomes incredibly frustrating to order and control their appearance since their controller can reside within another fragment's bounding box, making it select that controller automatically.

We just released a major redesign of the fragment mode to address a few different issues:
1. There’s a new sidebar where you can see all elements on the slide listed out. This lets you reach overlapping elements and enables you to create nested fragments (useful for nested bullet lists).
2. As soon as there are two or more fragments, a new interface will appear that allows you to preview fragments without leaving the current view.
3. There’s a new button for resetting all fragments.
Let us know if you run into any issues or have any comments.
Thanks!
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Arno Nym commented
It would be great to have a separate fragment editor which provides an overview of all elements of the current slide similar to the Inspector tool in Firefox (Ctrl + Shift + C) together with the current fragment configuration for each element (that is number, effect, ...). Similar to the Firefox Inspector, hovering over an element in the list would highlight the corresponding element on the slide to make identification easy. Also nested elements can be collapsed within the list for the sake of clarity. Then one could easily configure the elements of a slide as fragments no matter how they are arranged and not having to bother with point and click on the slide itself which can be everything from tedious to impossible based on how the elements are arranged.
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Felipe Delestro commented
This is true. Usually I need to place all the objects far apart, apply the fragment order and then move them back to the original position.
@Billy Mathews: To disable the fragment, just click on it again while on the fragment edit mode
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Billy Mathews commented
Also, once you have set something to be a fragment, I can't find any way to then disable it.
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Anonymous commented
Also, going back into fragment mode seems to reset all of their relations to one another. It makes testing things out and doing iterations a nightmare, as you have to continually redo what you just did.