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The GNU Makefile Standards specify a number of different clean rules. See See Standard Targets for Users in The GNU Coding Standards.
Generally the files that can be cleaned are determined automatically by
Automake. Of course, Automake also recognizes some variables that can
be defined to specify additional files to clean. These variables are
MOSTLYCLEANFILES, CLEANFILES, DISTCLEANFILES, and
MAINTAINERCLEANFILES.
As the GNU Standards aren’t always explicit as to which files should be removed by which rule, we’ve adopted a heuristic which we believe was first formulated by François Pinard:
make built it, and it is commonly something that one would
want to rebuild (for instance, a .o file), then
mostlyclean should delete it.
make built it, then clean should delete it.
configure built it, then distclean should delete it.
maintainer-clean should delete it. However
maintainer-clean should not delete anything that needs to exist
in order to run ./configure && make.
We recommend that you follow this same set of heuristics in your Makefile.am.