In several projects I have seen the Makefile.in without Makefile.am . E.g. bash http://git.savannah.gnu.org/cgit/bash.git/tree/ and dtach http://dtach.cvs.sourceforge.net/viewvc/dtach/dtach/
I always thought that Makefile.in was generated by automake. Also with Makefile.am being a user written file I would not have thought it would be omitted from the code repository. In the bash source tree, the Makefile.in is far too big to be hand written and the Makefile.in in dtach also looks generated. How was the Makefile.in generated in projects like these two?