FakeReader: detect multi-file screens from any of the field files

Prior to this, multi-file screens could only be detected from the
top-level directory.  This meant that importing into OMERO would not
have the desired effect, as ImportCandidates automatically recurses into
the directory and picks up the individual field files.

Fixes #12430.
mkfake: prevent the top-level directory name from being just ".fake"

See #12430.  It's a little weird to have e.g. 'mkfake ~/' create
~/.fake/, and makes it a little more difficult to find or remove the
screen directory.  'mkfake ~/' with this change will now create
~/screen.fake/, or ~/screenX.fake/ where X is the smallest index (from
1) for which a directory does not exist.
FakeReader: allow each channel's color to be specified separately

The 'color_x' keys (where x is the channel index) now set the color for
the specified channel.  These keys can be used with 'color', which acts
as a default value for any missing or invalid 'color_x' values.

Fixes #12423.
Fix used file listing for multi-file screens
Add HCS domain when fake image is SPW.
Merge pull request #16 from bpindelski/add-domains

Add HCS domain when fake image is SPW.
Do not create empty Channel objects
Make sure that extra files do not end up on the used file list
merge develop -D org: PR 983 (Woolz: make sure the service is initialized when calling openBytes (rebased onto develop))
merge develop -D org: PR 1154 (Leica: prevent exception when linking EmissionFilter)
merge develop -D org: PR 1191 (FakeReader improvements, part 1)
merge develop -D org: PR 1205 (TIFF: correctly account for ```fakeBigTiff``` when reading IFD entries)
merge develop -D org: PR 1208 (docs: Merge xsd-fu prerequisites into build instructions (develop))
merge develop -D org: PR 1209 (ND2: fix tile reading when the X coordinate is > 0)
merge develop -D org: PR 1210 (Zeiss LSM: fix offset calculationg for > 4GB files with SizeT > 1)
merge develop -D org: PR 1211 (Close IFormatReader copy if not to be used (rebased onto develop))
merge develop -D org: PR 1212 (Fix Z and T size calculation for InCell 6000 data)
merge develop -D org

Repository: openmicroscopy/bioformats
Excluded PRs:
  # PR 1141 LeeKamentsky 'Reader for Amaris FlowSight .cif format' (label: exclude)
  # PR 1200 melissalinkert 'Fix off-by-one in LZW decoding' (status: pending)
  # PR 978 berl 'Add writing of .v3draw format for easy loading with Vaa3D.' (user: berl)
  # PR 1177 rleigh-dundee 'specification: Add metadata for HDF5 embedding' (exclude comment)
  # PR 1015 qidane 'Messy binary' (exclude comment)
  # PR 1204 rleigh-dundee 'cpp: Add PixelBuffer<> and VariantPixelBuffer' (exclude comment)
  # PR 1161 sommerc 'Initial CellH5 Reader class' (user: sommerc)
  # PR 857 melissalinkert 'Initial support for Zeiss .lms files' (label: exclude)
  # PR 1054 qidane 'Additional annotation points throughout the model' (exclude comment)
  # PR 816 melissalinkert 'Add support for multi-channel Volocity Clipping datasets' (label: exclude)
  # PR 858 melissalinkert 'Initial support for Veeco AFM data' (label: exclude)
  # PR 1136 melissalinkert 'Add initial support for reading BinaryOnly OME-TIFF datasets (rebased onto develop)' (label: exclude)
Updating cc0474c..f6f048a
Merged PRs (fast-forward):
  # PR 1199 melissalinkert 'Nikon .nd2 fixes, part 3 (rebased onto develop)'

Merged PRs:
  # PR 983 melissalinkert 'Woolz: make sure the service is initialized when calling openBytes (rebased onto develop)'
  # PR 1154 melissalinkert 'Leica: prevent exception when linking EmissionFilter'
  # PR 1191 melissalinkert 'FakeReader improvements, part 1'
  # PR 1205 melissalinkert 'TIFF: correctly account for ```fakeBigTiff``` when reading IFD entries'
  # PR 1208 rleigh-dundee 'docs: Merge xsd-fu prerequisites into build instructions (develop)'
  # PR 1209 melissalinkert 'ND2: fix tile reading when the X coordinate is > 0'
  # PR 1210 melissalinkert 'Zeiss LSM: fix offset calculationg for > 4GB files with SizeT > 1'
  # PR 1211 joshmoore 'Close IFormatReader copy if not to be used (rebased onto develop)'
  # PR 1212 melissalinkert 'Fix Z and T size calculation for InCell 6000 data'
Generated by OMERO-5.1-merge-push#328 (http://ci.openmicroscopy.org/job/OMERO-5.1-merge-push/328/)