Base: Remove the empty /usr/lib and /usr/include directories

These have been there since the initial revision of the toolchain build
script, but we don't seem to require them being present in `Base` any
longer.

Base/usr/include/.gitignore

@@ -1,2 +0,0 @@
-*
-!.git*

Base/usr/lib/.gitignore

@@ -1,2 +0,0 @@
-*
-!.git*