openfoam: avoid lagrangian and region name ambiguity

- now prefix all non-default regions as "/regionName/...".
  The default region has now prefix. This eliminates any
  possible ambiguity if we happen to have slightly odd
  region names like "patch", "lagrangian", "internalMesh", ...

- drop old OpenFOAM 1.3 cloud naming.
  These were simply dumped into the time directory without any region
  qualifications. Defunct since about 2007.

- additional code comments explaining some of the structures