To compile under Linux.
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just run :

./bootstrap
./configure --with-mp4v2
make
sudo make install


about the xmms plugin.
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 The xmms plugin need to be build after the install of the faad project.
so after you have installed correctly faad (--with-xmms options) you need
to configure and build the xmms plugin part in the plugins/xmms directory.
Read the README and INSTALL files into the xmms directory.