Allow Dependency objects to be marshaled

When an exception is raised in the build process, it is marshaled and
sent to the main process over a pipe. The marshaled exception has
a reference to the formula, so the formula and all objects it references
are marshaled as well.

Previously this did not include dependencies, as they were stored only
on the class and not referenced by an instance variable. However, now
they are stored on SoftwareSpec instances, to which the formula *does*
have a direct reference, so they must be marshalable.