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Right now my current solution is using the outlines package in LaTeX with some fancy scripting in the sublime text editor to manipulate my outlines similar to the way you can promote demote and reorder the outlines in omnioutliner.

I really want a way to better use equations in omnioutliner. I find latexit very fragile. It hangs all too often to be reliable. I have to take notes on thousands of pages with math in them and my career depends on me studying/using these notes.

I think my ideal workflow would be to put the text representation of the equation in the notes section for a particular cell, then loop over all cells, see if there is an equation in the notes, render it as a picture, then place it in the cell. This way I can always be sure to have the equation as text if anything goes wrong.

I haven't given up yet and I will be sure to post anything I come up with.