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GNU Autotools
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Ick.
Setting up autotools
autoreconf can be used on initial setup, or after the autotools installation has been modified. Use -f to force refreshings, and -i to install missing files; autoreconf -fi is thus a useful recipe for source trees.
Local macros
Put them in acinclude.m4, *not* aclocal.m4. The latter is blown away by autoreconf. The former is properly included along with aclocal.m4 (which ought be automatically generated by aclocal) by autotools.
Alternatively, you can use multiple files in a subdirectory, and then use AC_CONFIG_MACRO_DIR([dirname]) (and ACLOCAL_AMFLAGS=-I dirname in Makefile.am).
