Long ago I wrote a version of WinPicProg that had a simple in-built BASIC compiler, this generated assembler code, and then called MPASM to assemble it, the resultant HEX file was then automatically loaded back in to WinPicProg, and (optionally) automatically uploaded to the target PIC.
I can't really remember now?, but I suspect as part of that process any extraneous files were deleted - no command line flags or whatever, just done in the Windows source code.