Use the last n detector gains and offsets

This fixes the detector index so that the last n gains and offsets are
used, instead of the first n.

See #7897.
Check MicroManager metadata files more thoroughly

...so that we do not inadvertantly pick up files that do not really
belong to MicroManager datasets.

Noticed by Tom Kazimiers.
Fix configuration file path name checking

This allows the data tests to run again.
Only overwrite the channel count for non-RGB data

The user is allowed to do whatever they want to the dimensions in
ImageJ; sometimes, this means that the channel count is changed to 1
when RGB data is actually stored in the file.

Noticed by Tom Kazimiers.
Create log files as soon as possible
Add some extra diagnostics to the log file

The hope is that this will help to track down why a particular directory
is detected as being invalid.
Stop parsing tags if we have reached the EOF

Noticed by Anthony Luu.
Flip the planes upside-down

In carefully re-reading the MRC specification, the image origin is
assumed to be in the lower left corner (not the the upper left corner).
To correct for this, we now reverse the order of the rows prior to
returning the image.
Allow units to be specified as "micrometers"

Previously, only "um" and "microns" were allowed.  Since it's all the
same unit, allow "micrometers" too.

Reported by Glen MacDonald.
Fill in missing units for the C axis

Some software (notably Huygens) does not feel the need to write a unit
for the C axis.  This causes our poor ICS reader a great deal of
confusion, as the index into the array of units is now wrong.  So now we
check for a missing unit, and add in "nm" for the C axis as appropriate.

Reported by Glen MacDonald.
Parse the slice spacing and populate PhysicalSizeZ
Add missing 'break' statements

Noticed by FindBugs.
Add missing null check for the ND2Handler

Noticed by FindBugs.
Fix outdated statements in the readme files

The top-level directory is now 'components/scifio', and Maven 3 is
supported as of earlier today.
Be sure to remove singleton files with no Z index

This prevents an ArrayIndexOutOfBoundsException when a single extra file
is placed first on the list of used files.

Reported by Helio Roque.
Do not convert OTF elements

The OTF element was deprecated in the 2011-06 OME-XML schema.  As it is
deprecated and often written incorrectly, we now no longer convert it.

See #7886.
Fix possible NPE

Introduced in f5fe876da0b5373a3230b250f8567cc4e1fdf04e.
Ensure that the tile dimensions are not too large

The last tile in a row or column is often smaller than the optimal size.
Instead of just assuming that the optimal dimensions will work, we
adjust the width and height of the last tile as needed.

This should fix all sorts of failures in the BIOFORMATS-openbytes-performance
Jenkins job.
Add '-no-sas' option, to disable SA display

See #8148.  Using the '-no-sas' option with '-omexml' will print OME-XML
that has the StructuredAnnotation elements removed.

To test, verify that 'java loci.formats.tools.ImageInfo -omexml file'
displays StructuredAnnotations, while 'java loci.formats.tools.ImageInfo
-no-sas -omexml file' does not.
Add '-xmlspaces' option for specifying indentation

Previously, 3 spaces were used for indenting OME-XML.  This isn't
optimal for all use cases, so now we allow the number of spaces to be
specified, e.g. '-xmlspaces 4'.  See #8147.