Supporse the emacs version in apt repository is 24.3, I configure && make install my own emacs 24.4. After a long time, the software in apt repository updated to 24.5. What would apt do when I run apt-get update && atp-get safeupgrade?
What's the general way to let apt handle my manual installed software?
Using
configure && make installis not installing a software package, so apt doesn't notice or care. If you see that there is an update, remove your manually built code and runsudo apt update && sudo apt upgrade. Apt CAN NOT manage your manually built software unless you install it as a package. Use this to create your own packages: https://wiki.debian.org/HowToPackageForDebian.