Preparation for de-duplicating mdrun setup

Preparation for de-duplicating mdrun setup

Recent work introducing the API extracted MdFilenames and then
essentially duplicated everything else. This commit expands
MdFilenames into LegacyMdrunOptions, and clarified the plan that all
such code needs to become either module-based option handling, or
aspects of SimulationContext suitable for both CLI and API.

This commit introduces the Legacy MdrunOptions struct, so that a
future commit can make it available to the API setup for an mdrun
session. The layout of the changes is intended to minimize the textual
diff for the CLI. Code motion for clarity and also use by the API will
follow.

Removed MdFilenames, made its data a std::vector in
LegacyMdrunOptions, and used it via an ArrayRef. This clarifies that
it is read-only input data supplied by the client.

Change-Id: I3438cfe1ab52eeb2fffbd16f4bd5254b2a74f03f