gpgme puts its config.h in conf directory.
Current Automake doesn't handle this case correctly for the dependency to config.h generation.
For example, when configure.ac is touched, config.h.in won't be generated by make invocation.
Possible fix is either of:
(1) put config.h in the top directory. Then, Makefile includes the dependency all: config.h
(2) create conf/Makefile.am and add conf/Makefile in configure.ac, and add the conf directory to SUBDIR in the top Makefile.am