It appears that I sometimes get the following error saving code to a connected server:
e.g., 4:42 PM Deployment Failed: DUPLICATE_VALUE - duplicate value found: <unknown> duplicates value on record with id: <unknown>
Annecdotally, I seem to only get them with Apex Classes, but once I get them, I can no longer deploy the files for which I received the error.
Copy/pasting the code into the Developer Console and saving that way returns no errors and I'm able to save successfully.
Using 22.214.171.124 of IlluminatedCloud Using IDEA 2016.3 (163.7743.44, built 11/17/2016) Host OS: Mac OS X 10.12.1