Flex: improved metadata handling

This fixes field counts for large plates with one file per field, makes channel metadata consistent across wells/fields, and removes redundant MetadataStore calls.  The xsd-fu template changes should slightly reduce the time needed to populate model objects (which should reduce setId and OMERO imports times).

Aside from builds being green, it might be useful to import one of the larger plates (e.g. ```flex/christophe``` or ```flex/anatole/Meas_05(2012-05-16_18-51-33)``` into OMERO to verify that performance is no worse with these changes.
Does the C++ implementation also require updating to behave in this way?  I can open a PR against this if so.