Refactor namelist modification

[dafyddstephenson]

Closes #118 . Branched from #117 , merge #117 and update diffs before review (should be +209, -123)

This PR:

• adds a ROMSComponent._namelist_modifications property (list[dict]) "parallel" to ROMSComponent.namelists that tracks needed modifications to the template file based on the state of ROMSComponent
• adds an update_namelists method to ROMSComponent that makes a new set of modified namelist files based on the current values in the _namelist_modifications property.
• Moves all namelist modification to immediately before runtime, in ROMSComponent.run()

[dafyddstephenson]

Tests are failing as pytest code has diverged. Will be corrected after merging #108 .