How do I locally run and publish a script that resides in a different directory?

I am trying to use a Linux shell script to repeatedly publish a Matlab .m script (that calls multiple sub-scripts and functions from a common subdirectory). I also need it to read user input (in .m format) from a seperate working directory and create the output in that working directory. I can't seem to get Matlab to keep track of both directories (i.e. the "source" directory and the "working" directory). The "source" directory (and subdirectory) should be constant and read-only. The "working" directory should be the directory I am currently in which contains the shell script I am using to run/publish the code and my input files.

Essentially what I want to do is treat the source script(s) as if it were a compiled executable for QA purposes without actually compiling it (since publish doesn't work with compiled code). I want to store the main code in a designated location and run it from my working directory multiple times with diferent input file selections.