Last round of fixes for working with mapped files

This is necessary to make the required directory tests pass.
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 1296 (Add test for getRequiredDirectories)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 1363 (C++: Add TIFF strip/tile write support)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only: PR 1364 (Adding external PR guidance to CONTRIBUTING.md)
merge develop -Dorg -Ijburel/openmicroscopy:qa-submit-new -Ssuccess-only

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1177 rleigh-dundee 'specification: Add metadata for HDF5 embedding' (exclude comment)
  # PR 1309 melissalinkert 'Allow tile-based access of large JPEG-2000 images' (exclude comment)
  # PR 1265 qidane 'New units' (label: breaking)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 1362 melissalinkert 'Make FormatReader's RandomAccessInputStream transient' (label: breaking)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (label: exclude)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (label: exclude)
  # PR 1161 sommerc 'Initial CellH5 Reader class' (user: sommerc)
Already up-to-date.

Merged PRs:
  # PR 1296 melissalinkert 'Add test for getRequiredDirectories'
  # PR 1363 rleigh-dundee 'C++: Add TIFF strip/tile write support'
  # PR 1364 hflynn 'Adding external PR guidance to CONTRIBUTING.md'

Generated by OME-5.1-merge-push#507 (http://ci.openmicroscopy.org/job/OME-5.1-merge-push/507/)