I created a file tree that looks similar to my system’s file tree, except it only contains all the files that I modified or added and only their respective directories. From there I just use rsync to sync those files/file tree to the system’s /.

It’s convenient to see what changes I currently have but it requires a bit of manual maintenance. I only really started doing it that way because I was learning how to use rsync and I just kept going on with it because it was working for me.

I’m only working with my laptop, android phone and two Raspberry Pi’s so I can get with my little rsync based setup.

I haven’t tried it myself but https://wiki.termux.com/wiki/Termux:Boot seems to be able to start Termux and programs after a phone starts/reboots. It does require downloading an additional package https://f-droid.org/packages/com.termux.boot/ along with the main Termux app.