Though not simple, it is doable.
I can build you a "service" for that, which runs on boot (as soon as the machine turns on) with whatever configuration you want. That way you can configure it once and it will continuously run even after rebooting the computer, without further human input, or having to run the program again.
The only problem I foresee is recognizing which files contain text, so that the program understands to track line-code in each. This can also be problematic if you have very large files, since the program needs to keep backups of each file for comparison. I might be able to suggest a more elegant solution if I better understood the nature of the files to track.
Lastly, I'd like to explain that file extensions don't control the file, but are a suggestion of how to use them. You can treat an exe as text, and vis-a-vis, or entirely forgo assigning an extension and use it as you please. I say this because it'd be easy for someone to change the extension of a file and suddenly bypass this program's security as you asked. It's far more convenient to embbed tracking numbers in the meta-data of the files themselves. This approach is harder to implement, but far more secure.
I'd very much like to keep talking, but I'm running out of characters in this bid. Feel free to contact me with any questions or doubts. I can help you plan this project even before you accept my bid, no strings attached.
Hope to hear from you soon,
Joel Villasuso