This patch changes the clean target to clean up the makefiles by running autoreconf -if. If I understand correctly, this just resets the build artifacts to match the gnutools installed. The compile-native target now also does and autoreconf, just like the c++ targets do.
If you do either of the following commands, the build now works correctly.
ant -Dcompile.c++=true -Dcompile.native=yes -Dlibhdfs=true clean compile-native compile
ant -Dcompile.c++=true -Dcompile.native=yes -Dlibhdfs=true clean compile compile-native
(My assumption is that non-c++ and non-native targets aren't impacted by this change.)
It needs to be applied in addition to the previously committed patch. This patch also works, with some "fuzzing" on the 0.20 branch.