Re-organize developers documentation index
Split using-bioformats file
Rename contributing sections
Limit maxdepth of main index page
Split the troubleshooting sections
Rename section about writing a new reader
Merge pull request #1376 from sbesson/developer_doc_restructuring

Developer doc restructuring
merge develop -Dnone -Ibreaking -Eexclude -Ssuccess-only: PR 1362 (Make FormatReader's RandomAccessInputStream transient)
merge develop -Dnone -Ibreaking -Eexclude -Ssuccess-only

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1161 sommerc 'Initial CellH5 Reader class' (user: sommerc)
  # PR 1379 melissalinkert 'New units' (status: pending)
  # PR 1375 rleigh-dundee 'C++: Documentation updates' (user: rleigh-dundee)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (user: melissalinkert)
  # PR 1365 ctrueden 'PrairieView 5.2 fixes and improvements' (user: ctrueden)
  # PR 1378 melissalinkert 'DICOM: also use the pixel sign tag to detect the pixel type' (user: melissalinkert)
  # PR 1309 melissalinkert 'Allow tile-based access of large JPEG-2000 images' (exclude comment)
  # PR 1381 melissalinkert 'Parse physical pixel sizes from CellSens .vsi datasets' (user: melissalinkert)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (user: melissalinkert)
  # PR 1366 ctrueden 'Miscellaneous cleanup' (user: ctrueden)
  # PR 1177 rleigh-dundee 'specification: Add metadata for HDF5 embedding' (exclude comment)
  # PR 1015 qidane 'Messy binary' (exclude comment)
Updating 5706a61..6a074dd
Previously merged:
  # PR 1376 sbesson 'Developer doc restructuring'
  # PR 1377 hflynn 'Replace BigTiff sample link'
  # PR 1374 rleigh-dundee 'C++: Collected small fixes'
  # PR 1373 rleigh-dundee 'cpp: test: Only test multi_array assertions for release builds'
  # PR 1369 sbesson 'Document usage of setSeries() and getIndex() in MATLAB documentation'
  # PR 1371 rleigh-dundee 'C++: Read and write all pixel types and validate all tags and pixel data'
  # PR 1296 melissalinkert 'Add test for getRequiredDirectories'
  # PR 1370 rleigh-dundee 'cpp: Adapt to Boost 1.56 optional changes'

Merged PRs:
  # PR 1362 melissalinkert 'Make FormatReader's RandomAccessInputStream transient'

Generated by OME-5.1-breaking-push#135 (http://ci.openmicroscopy.org/job/OME-5.1-breaking-push/135/)