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
ND2: ignore invalid image offsets

Fixes QA 7534, #11305.
ND2: rework text annotation parsing so that dimensions are not overlooked

Fixes #12205.
ND2: set SizeT to the number of offsets if there is no dimension metadata

See #10773.
Do not adjust offset count if only one offset is present
One more fix to prevent equal-size planes from being ignored
Fix channel metadata population for multi-series data
Fix off-by-one in LZW decoding

See
http://lists.openmicroscopy.org.uk/pipermail/ome-users/2014-July/004566.html
TIFF: correctly account for fakeBigTiff when reading IFD entries

Fixes #12367.
docs: Merge xsd-fu prerequisites into build instructions

Merge source code page with build instructions
Move build instructions to the top since it's got a wider
scope than contributing--non-developers need this
docs: Correct incomplete sentence
docs: Correct genshi notes
docs: Simplify crossreference
docs: Rework git links