MPLABX + PICKit 2 programmer could not be started
It seems that some PIC devices are partially supported by MPLABX (e.g., PIC16F1829). You can recognize this when creating the project: in the dialog where you select what tools you use, if the icon to the left of PICKit2 is yellow, then it's not possible to program the device directly from MPLABX, and the error message is the one you mentioned here. Only the standalone app can be used to program the MCU. If the icon is green (e.g., with PIC16F690), no problem. The workaround is to create a script (or .bat file?) that uploads the code to the PIC.

I haven't had any problems with reading through the standalone app though.