Fix multi-file export in ImageJ

Closes #9829.
Cellomics: only do a directory listing if we are grouping files
TileStitcher: attempt to stitch even if PositionZ varies

Fixes #9378.
Zeiss LSM: make the .mdb file checking a bit more strict

Fixes #9807.
DICOM: correctly reverse endianness when necessary

Fixes #9870.
2008-09: update CustomAttributes to StructuredAnnotations
Try harder to parse original metadata from XMLAnnotations

If the XMLAnnotation does not contain an OriginalMetadata node, then we
look for any nodes that have a "Value" attribute.

See #9905.
Zeiss CZI: fix gain and zoom population

Noticed by Martin Spitaler.
TIFF: handle IFD entry arrays with size 0

Fixes #9929.
Prevent ClassCastException when reading the IFD description

Conflicts:

	components/bio-formats/src/loci/formats/in/MetamorphReader.java

Conflicts:

	components/bio-formats/src/loci/formats/in/MetamorphReader.java
AVI: ensure that MSV1 images are detected as having 3 channels

Fixes the file in cellsens/samples/Fluorescence.
Metamorph: fix compile error

Conflicts:

	components/bio-formats/src/loci/formats/in/MetamorphReader.java
Prevent NPE when parsing XMLAnnotations
OME-TIFF: log isThisType exceptions at DEBUG
Only transform CustomAttributes if it has child nodes
CellR: fix handling of .apl files with "_" in the name

See QA #4789.
Fix conflict resolution that prevented streams from being closed
Reorganize extlinks and allow to pass SOURCE_USER for Github links

Reorganize extlinks to mirror organization of conf.py of ome-documentation.git
Fix Bio-Formats Jenkins job alias
Merge pull request #318 from melissalinkert/pr201-develop

PR 201 on develop