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Go to Class, Custom ability create your arcana in available to classes select you class,
below that select special ability category select Magus arcana or what you have chosen to call it. [The reason you are not getting any thing to select is that you have not told the program what to select in the special ability category] you will also more than likely have to write an eval script for what the arcana does. This should fix the issue you are having.
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