So I have searched for a program that can track file changes of a system.
I am using Debian based system and I'm well aware of using Apt to look into a deb file to see the paths, but what if im install something from a Shell script, Python script or using (C)Make Install.

What if its on Arch or Centos?

What I'm essentially looking for is a software that hashes the files of the system and then can tell me what has changed given the start of a installation and the end, It obviously dosen't have to track changes in /dev, /proc or any folders that are for running operations, onyl storage is what im looking for. Does any type of software like this exist?

It doesn't strictly have to work in the method I just suggested but I'm only stating that the way I think it might work, their probably is a much better solution that im not thinking of.

google is your friend
https://unix.stackexchange.com/quest...in-a-unix-host
https://github.com/emcrisostomo/fswatch

Ahh, Obvious! I tried Google but wasn't sure what to type in. My searches and asking about ultimatly lead to look into Intrusion Detection Systems for monitoring which files are being used.

Nothing will tell you what changed (as in what data), merely that the files changed - and/or (dis-)appeared. Nor can you directly correlate that to a particular action - unless it is the only action taking place for the entire time of interest.
You can get close, but not what you requested in a general sense. I use filesystem snapshot to enable me to roll-back my attempts to clean up photos. If I screw up I merely go back to the snap I took before I started - else I delete the snap. Simple. But the photos are on a separate filesystem that supports snapshot - that's native snapshot, not a hack using hard links. Tools like snapper generalise this to a system filesystem - but look at how complex opensuse make things to accommodate roll-backs.

Nothing is ever as simple as it first seems.

Tripwire ?
https://www.linux-magazine.com/Onlin...-with-Tripwire
https://www.tecmint.com/install-trip...stem-on-linux/

If you do want to follow this up, maybe ask the Mods to shift this to the 'Security' forum.

OT:
Correct.
The search phrase used to obtain a helpful link is just as important as the helpful link itself.
And fwiw, I use startpage.com. It should(tm) return non-personalised google results.

I entered the text from the first post: "track file changes of a system" and added only one keyword, linux.

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