i do mine a little old school 
i keep a libreoffice document called “bodhi fresh install” (pretty sure i got that idea from @ElectricDandySlider) and do my best to add things to it when i make changes to my system. there was a previous discussion here about trying to come up with a list of installed applications after the fact. this was chosen as the solution. Abhishek also offered a suggestion before that one. i have not run that script myself to verify, but it’s just a dpkg-query so it doesn’t make any kind of changes to your system.
most program mods or configuration changes (all maybe? well, probably some in /etc too now that i think about it, but definitely don’t copy that) are stored in your /home/user directory. my understanding is that is why some people choose to create a separate /home partition when they install. i have never done so. again, i default to my list and just go about setting up things like they were previously 