Refactor core::run in order to address many of the issues...

...mentioned in #2625.

This change makes the module more oriented around
Process values instead of having to deal with process ids
directly.

Apart from issues mentioned in #2625, other changes include:
- Changing the naming to be more consistent - Process/process
  is now used instead of a mixture of Program/program and
  Process/process.
- More docs/tests.

Some io/scheduler related issues remain (mentioned in #2625). I am not sure how best to address these.