Makefiles: change checkout and patch applying methods

The idea behind is that instead of checking out only the specific files, we checkout the whole repository because in U-Boot for example I am adding a new file with the patch and git checkout fails... The same would have happened for FSBL if instead of copying the files in the sources, we were adding them as a patch.

While at it, changing the patch approach to git am, to use git oriented patch mechanism and not just a bare diff file. The patch should fail if it is modified or if the sources are modified.

Signed-off-by: Vasileios Amoiridis vasileios.amoiridis@cern.ch

Closes #95 (closed)