Move all autotools helper scripts to auto-aux/

Move all autotools helper scripts and auxiliary files installed
automatically by the autotools to auto-aux/ (e.g. config.guess,
depcomp, install-sh, texinfo.tex, etc.).

Moving AC_CANONICAL_TARGET after AC_CONFIG_AUX_DIR works
around a silent bug in Autoconf 2.69 where the generated
configure script would not find the install-sh file which
has been placed in that given aux directory.

Moved AM_INIT_AUTOMAKE which must also happen after
AC_CONFIG_AUX_DIR.

src/auto-aux/.gitignore

@@ -0,0 +1,2 @@
+# Ensure git creates empty directory for autotools to place files into
+*

src/configure.ac

@@ -27,14 +27,16 @@ AC_INIT([avrdude],
         m4_esyscmd([./build-helpers/package-version . version-stamp]),
         [https://github.com/avrdudes/avrdude/issues])
 
+AC_CONFIG_SRCDIR([main.c])
+AC_CONFIG_HEADERS([ac_cfg.h])
+AC_CONFIG_AUX_DIR([auto-aux])
+AC_CONFIG_MACRO_DIR([m4])
+
 AC_CANONICAL_BUILD
 AC_CANONICAL_HOST
 AC_CANONICAL_TARGET
 
-AC_CONFIG_SRCDIR([main.c])
 AM_INIT_AUTOMAKE([foreign])
-AC_CONFIG_HEADERS(ac_cfg.h)
-AC_CONFIG_MACRO_DIR([m4])
 
 # Check that the build-helpers/package-version script has worked properly.
 case "$PACKAGE_VERSION" in