Gentoo's package manager (Portage) deals with this quite nicely for packages like st [1]. Both custom patches and config.h changes can be saved in the package

Gentoo's package manager (Portage) deals with this quite nicely for packages like st [1]. Both custom patches and config.h changes can be saved in the package manager, which will then apply them automatically to new versions. [1] https://packages.gentoo.org/packages/x11-terms/st https://packages.gentoo.org/packages/x11-terms/st