The feature of adding the program to the system startup requires Python to be installed globally because it copies a python file to the startup folder.

Two possible solutions would be to create a link to the program and put that into the startup folder or create a batch file that does the same thing as the python file.
I haven't been able to create a link through python but if that can work it would be the best solution.
The batch file is a possibility and I originally used it instead of the python file but it means that a command line will be displayed for about a second when it gets run.

To improve the speed of the algorithm it would be good to stop scanning files that are inside of a folder that is already hidden or marked to be hidden