ImageJ: disable file grouping when not reading from the filesystem

In particular, this disables grouping when reading over HTTP, as that is
at best extremely slow.

Fixes #12158.
ND2: adjust SizeC correction for small single plane datasets

Fixes #12222.
QuickTime: reset stream if an invalid atom length is found

This is particularly necessary if the "header" is at the end of the file.

Also clarifies a variable name that's been annoying me for a while, and
fixes a couple of typos.

Fixes #12218.
Metamorph: be less aggressive about closing readers right away

If the last plane has been read, or more than 128 readers are open, then
we can close the reader; otherwise, keep it open to prevent
reinitializing a reader on every openBytes call.

Fixes #11968.
Flex: fix whitespace annoyances
Flex: fix the case where one field is stored in each file

See #11382 and
http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2014-March/002721.html
Revert "CZI: restrict dimension adjustment"

This reverts commit f8ce7b1e749fe7d85d7fac1d2d547861166d3d43.
Flex: one more fix for dimension adjustment

The extra check for a valid image count is not necessary if only one
file is present in the dataset.
Flex: correct channel indexing when there is not one name per plane
Revert "Revert "CZI: restrict dimension adjustment""

This reverts commit f6ebfd82805ed6175a1ed693da1a9e3c10cd6c91.
merge develop -D org: PR 857 (Initial support for Zeiss .lms files)
merge develop -D org: PR 858 (Initial support for Veeco AFM data)
merge develop -D org: PR 981 (Ignore namespaces when filling in an XMLAnnotation's Value)
merge develop -D org: PR 983 (Woolz: make sure the service is initialized when calling openBytes (rebased onto develop))
merge develop -D org: PR 1028 (Large fileset performance improvements (rebased onto develop))
merge develop -D org: PR 1049 (DICOM: fix file grouping so that path names are normalized (rebased onto develop))
merge develop -D org: PR 1060 (Allow dist-matlab to run on Windows)
merge develop -D org: PR 1070 (DICOM: expand sequence reading to include known sequences (rebased onto develop))
merge develop -D org: PR 1082 (C++: Add support for integers of different endianness)
merge develop -D org: PR 1092 (Allow for a >1 count increment in B&H .sdt Files. (rebased onto develop))