I know you can compile PBP in later versions of MPLABX... I just tried it using MPLABX V3.60 and it works.
Not so sure about using things like the debugger or simulator, but I haven't used PBP much in a long time.

You need to keep MPLABX updated to support newer chips. You can choose to install just the IPE and that should get you newer part support for programming. MPLABX allows you to install multiple versions so you can always keep v2.35 around too.
Installing the IPE should get you the command-line tools.

MPLABX/IPE is the only programming tool (from microchip) that will be updated, so we're sort of stuck with it you want to use the Pickit3.