Delegate file updating logic to updateOriginalFile

All the logic for setting the name, size, uploading bytes and performing
checksums should now be handled in updateOriginalFile. This function is called
by writeFileAnnotation as well as updateFileAnnotation.

OME-DCO-1.1-Signed-off-by: Sebastien Besson <seb.besson@gmail.com> (github: sbesson)
Fix call to updateService in writeFileAnnotation

OME-DCO-1.1-Signed-off-by: Sebastien Besson <seb.besson@gmail.com> (github: sbesson)
Tidy up the M files (unused variables, semicolon)

OME-DCO-1.1-Signed-off-by: Sebastien Besson <seb.besson@gmail.com> (github: sbesson)