In some situations, the dependency tracking files in .deps can refer to
source files that were removed or renamed, leading to errors like:
make: *** No rule to make target `version.c', needed by `version.o'. Stop.
This patch makes the clean target clear the .deps directory, which gives
the user a chance to recover from the error wihtout knowing about the
internals of the build system.
It is already done for GDB. See here for more details: