To allow PICkit 3 to work with Flowcode 4 you must first update Flowcode to the latest version. This can be done by going to Help >> Check for Updates within Flowcode.

For Flowcode v5, this is automatically included.

Then in Flowcode click on Chip -> Compiler options.

Click the Programmer Tab.

Set the Programmer location to:

 C:\Program Files\Matrix Multimedia\Flowcode V4\Tools\PICkit3\pk3cmd.exe

Set the Programmer parameters to:

 -P%p -F%f.hex -E -M -Y

This configures the PICkit 3 to program the target devices using the project hex file. The PICkit will erase the device, fully program the device and then verify the data has been programmed correctly onto the device.

To allow PPP to provide configuration settings simply leave the Use external program to set config options setting ticked and leave the details as.

Location

C:\Program Files\Matrix Multimedia\Flowcode V4\Tools\PPP\PPPv3.exe

Parameters

-cs 2 -chip PIC%p -config

Some users have reported problems when using the settings listed above. They get the error "hex file not found".
Changing the programmer parameters to this seems to fix this problem.

-P%p -F"%f.hex" -E -M -Y"%f.hex"