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From that you can see that the problem is that bfd/, gas/, gprof/, libiberty/, and opcodes/ all use automake 1.9 / autoconf 2.59; whereas the toplevel and binutils/ use automake 1.4 / autoconf 2.13. It seems like no matter what incantation of WANT_AUTOCONF_2_1 and update-alternatives that you use, something will be unhappy as a result.
So it looks like a better way to go is to just run "autoreconf" in the subdirs that you want to regenerate, rather than configuring at the top level with --enable-maintainer-mode.
-- Chuck
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