Howto force UseLATEX to clean temporary files between changing configurations? [closed]

Question

I have a multiple-output LaTeX file, and created a CMake environment to produce all requested outputs as result of running a single command. Basically, it works. However, since I do have bibliography, index and glossary, but also the page number of figures, tables, etc. may change between formats, I would need to start a 'clean' build between the formats. Presently, I make individual main files for the different format in a foreach loop. Probably making auxclean between the individual formats could solve my problem, but I do not know how to reach it internally.