merging with the trunk

src/Doxyfile

src/Makefile

src/TODO

src/base/Makefile

src/configure

src/decoder/Makefile

src/doc/about.dox

src/doc/decoders.dox

src/doc/hmm.dox

src/doc/install.dox

src/doc/lattices.dox

src/doc/matrixwrap.dox

src/doc/model.dox

src/doc/tools.dox

src/doc/tree_externals.dox

src/doc/tutorial_code.dox

src/doc/tutorial_looking.dox

src/doc/tutorial_running.dox

src/doc/tutorial_setup.dox

src/feat/Makefile