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Makefile.am

Makefile.am is processed by automake.
The commands in a Makefile.am file mostly look like variable assignment.
Each directory in a package should contain an Automake.am file. This Automake.am in turn should specify its subdirectories like so: 
SUBDIRS = dir_foo dir_bar dir_baz
Each Automake.am file should have a corresponding AC_OUTPUT in the configure.in file.

Cygnus mode

To put automake into cygnus mode, add this line to Makefile.am: 
AUTOMAKE_OPTIONS = cygnus

???

bin_PROGRAMS = foo_prg
foo_prg_SOURCES = foo.c bar.c 

lib_LIBRARIES = libfoo.a
lib_foo_a_SOURCES = foo.c bar.c

lib_LTLIBRARIES = libfoo.la
libfoo_la_SOURCES = foo.c bar.c
bin_ and bin_ refer to directories specified with the configure options --bindir and --libdir.

????

AUTOMAKE_OPTIONS

See required files for automake.