You may have an empty directory in a subpackage, called, say, "shared", with a make file that copies external files. You can then use the dist-hook target to move the files directly to the version of the “shared” directory, which will be encrypted in tarball. This way, you don’t have to worry about them laying down and being edited. You also overwrite Makefile.am, Makefile.in, and Makefile in a “generic” way when copying.
Example in subpackage / common / Makefile.am (untested):
dist-hook: cp -p $(top_srcdir)/../common/Makefile* $(top_srcdir)/../common/*.[ch] $(distdir)
I am not sure that 100% this will work. This can break the rest of your package, depending on where everything else expects to find these source files; it will probably break if you unpack the archive and try to escape from there. You should know that this trick is disapproving. But I hope I have given you enough ideas to play with them.
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