In addition to obvious changes, this required a slight change to the slicc
grammar to allow types with :: in them. Otherwise slicc barfs on std::string
which we need for the headers that slicc generates.
This was done with an automated process, so there could be things that were
done in this tree in the past that didn't make it. One known regression
is that atomic memory operations do not seem to work properly anymore.
This basically means changing all #include statements and changing
autogenerated code so that it generates the correct paths. Because
slicc generates #includes, I had to hard code the include paths to
mem/protocol.
