Best practice to distribute a project?

I have a fairly large project which was written as a MATLAB Project (capital P), meaning that there exists a .prj file that I have to open before using or editing the code. Making this a Project allows me to set some preferences and add the source directories to the path. When the user closes the projet file, their default settings are restored.

The project is available for download and fairly well documented (I hope). For now, it remains in the form of a Project, so the user must open the .prj file in order to use the codes. The documentation explains that step one of running the code is opening this file.

I haven't seen other software distributed this way. Is this the way the Mathworks intends it to work or is there an additional step I can take that can relieve the user of this burden?