clean up object file build rule, and do not attempt to remove link_directories that are in the build tree

ENH: cmMakeDepend::GenerateDependInformation will now use hints regardless of whether the actual file exists.  This can be used to add dependencies to .h files which are generated but included in hand-written .cxx files.  If the .cxx does exist, though, it will be used first, and the hints will be used afterward.

Reimplement code. Since a custom command is very flexible and might be extended in the future, make all arguments prefixed with arg type, make ordering irrelevant and potentially all args optional.