[pm215]

Typically if a system header has changed or been added due to upgrading a library package you'll need to rerun any configure script anyway (since it very likely checks for header features and those decisions will change). So unless your build system magically makes configure depend on every header file used in every configure test it runs, you'll need to redo a clean build anyway, pretty much.

Make has a whole pile of issues, but this one really isn't an aggravation in practice, I find.

[beagle3]

apt-get upgrade does not usually upgrade a package, despite the name; 99.9% of the time it applies a bug or security fix, almost never changing any functionality or interface - and would result in the same config script.

And that assumes you actually have a config script, which is also a nontrivial assumption.

Djb redo lets you track e.g. security fixes that change libc.a if you are linking statically, but that's not usually done.

The only build system I know that guaranteed a rebuild whenever and only when it is needed is tup. (Assuming you have only file system inputs)