The usual way to regenerate the files that Automake maintains in a package is
or less conveniently:
aclocal # with any option needed (such a -I m4) autoconf automake --add-missing --force-missing
The use of --force-missing ensures that auxiliary tools will be overridden by new versions (see automake Invocation).
It is important to regenerate all of these files each time Automake is upgraded, even between bug fixes releases. For instance, it is not unusual for a bug fix to involve changes to both the rules generated in Makefile.in and the supporting M4 macros copied to aclocal.m4.
automake is able to diagnose situations where
aclocal.m4 has been generated with another version of
aclocal. However it never checks whether auxiliary scripts
are up-to-date. In other words,
automake will tell you when
aclocal needs to be rerun, but it will never diagnose a
Before upgrading to a new major release, it is a good idea to read the file NEWS. This file lists all changes between releases: new features, obsolete constructs, known incompatibilities, and workarounds.