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Every time Automake is run it calls Autoconf to trace configure.ac. This way it can recognize the use of certain macros and tailor the generated Makefile.in appropriately. Currently recognized macros and their effects are:
AC_CANONICAL_BUILDAC_CANONICAL_HOSTAC_CANONICAL_TARGETbuild_triplet,
host_triplet and target_triplet are introduced.  See
Getting the Canonical System Type.
     AC_CONFIG_AUX_DIRIf AC_CONFIG_AUX_DIR is not given, the scripts are looked for in
their standard locations.  For mdate-sh,
texinfo.tex, and ylwrap, the standard location is the
source directory corresponding to the current Makefile.am.  For
the rest, the standard location is the first one of ., ..,
or ../.. (relative to the top source directory) that provides any
one of the helper scripts.  See Finding `configure' Input.
     
Required files from AC_CONFIG_AUX_DIR are automatically
distributed, even if there is no Makefile.am in this directory.
     
AC_CONFIG_LIBOBJ_DIRAC_LIBSOURCE (see below) in the directory specified by this
macro.
     AC_CONFIG_HEADERSAM_CONFIG_HEADER
(see Macros); this is no longer the case today.
     As for AC_CONFIG_FILES (see Requirements), parts of the
specification using shell variables will be ignored as far as
cleaning, distributing, and rebuilding is concerned.
     
AC_CONFIG_LINKSAs for AC_CONFIG_FILES (see Requirements), parts of the
specification using shell variables will be ignored as far as cleaning
and distributing is concerned.  (There is no rebuild rules for links.)
     
AC_LIBOBJAC_LIBSOURCEAC_LIBSOURCESAC_LIBSOURCE or AC_LIBSOURCES.
     Note that the AC_LIBOBJ macro calls AC_LIBSOURCE.  So if
an Autoconf macro is documented to call ‘AC_LIBOBJ([file])’, then
file.c will be distributed automatically by Automake.  This
encompasses many macros like AC_FUNC_ALLOCA,
AC_FUNC_MEMCMP, AC_REPLACE_FUNCS, and others.
     
By the way, direct assignments to LIBOBJS are no longer
supported.  You should always use AC_LIBOBJ for this purpose. 
See AC_LIBOBJ vs. LIBOBJS.
     
AC_PROG_RANLIBAC_PROG_CXXAC_PROG_OBJCAC_PROG_F77AC_F77_LIBRARY_LDFLAGSAC_PROG_FCAC_PROG_LIBTOOLAC_PROG_YACCYACC in configure.ac.  The former is
preferred (see Particular Program Checks).
     AC_PROG_LEXAC_REQUIRE_AUX_FILEAC_CONFIG_AUX_DIR
above.  See Finding configure Input.
     AC_SUBSTIf the Autoconf manual says that a macro calls AC_SUBST for
var, or defines the output variable var then var will
be defined in each Makefile.in generated by Automake. 
E.g. AC_PATH_XTRA defines X_CFLAGS and X_LIBS, so
you can use these variables in any Makefile.am if
AC_PATH_XTRA is called.
     
AM_C_PROTOTYPESAM_GNU_GETTEXTAM_GNU_GETTEXT_INTL_SUBDIRAM_GNU_GETTEXT macro was invoked with a first argument
of ‘external’.
     AM_MAINTAINER_MODEMAINTAINER_MODE conditional, which you can use in your own
Makefile.am.  See maintainer-mode.
     m4_includem4_include is seldom used by configure.ac authors, but
can appear in aclocal.m4 when aclocal detects that
some required macros come from files local to your package (as opposed
to macros installed in a system-wide directory, see Invoking aclocal).