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I used to use an app called Afloat that let me pin windows on top of all other windows on the Desktop. However, Afloat stopped being maintained at some point and it doesn't work with more recent versions of OS X.
I then used an app called Compulsion, which installed as a SIMBL plugin but then that stopped working with OS X El Capitan.
Is there a way to get either of these apps to work with OS X El Capitan? Or is there another solution I can try?