Automatically Boolean STLs from the command line

We are looking to develop a script which automatically will modify Stl files and save the result: Given a folder location, the script will use an open source or licence free 3D modelling software to: -Automatically import stl files -Run a mesh repair if necessary -Use a suitable means to make a cuts (boolean difference or alternative) using the files provided -Discard unnecessary result from the boolean. -Join (Combine/boolean union) the result with another imported file and save it to the source folder -These operations must work robustly This will need to be run through the command line and will be used to process large batches of similar files with alternating dimensions C# programming and the ability to work use it to work with other programs (such as meshlab) would also be beneficial but is not a necessity. A successful candidate will outline their approach and the base program which they intend to use fo the 3D operations.