PrairieReader: handle any sequence numbering

PrairieView is capable of producing data where the cycle numbering does
not increment one at a time (e.g., for metadata with
cycle=2,5,8,11,...). We have not yet observed any datasets with
variable, non-linear increment patterns (e.g., cycle=2,4,5,11,12,...),
but this new approach should handle that too.

The new approach works by explicitly creating and sorting a list of
existing sequences, then using that list as the basis for sizeT & sizeP,
rather than assuming that Sequence#getCycleCount() will be sensible.
PrairieReader: fix handling of inverted Z/T

In the case where a Sequence is flagged as a TSeries, the Frames of that
Sequence must be treated as time points rather than focal planes. This
logic was previously not fully propagated through the code.
Leica LEI: improve setId performance

This primarily involves reading the entire .lei file into memory and
only calling list() when absolutely necessary.
Operetta: reduce setId execution time
CellWorX: minor setId performance improvements
CellR: reduce setId execution time
Canon RAW: reduce setId execution time
Leica: throw a nicer exception if TIFF files are not found
Merge remote-tracking branch 'origin/develop' into ndpi

Conflicts:
	components/bio-formats/src/loci/formats/in/HamamatsuVMSReader.java
	components/bio-formats/src/loci/formats/in/NDPIReader.java
Fix restart marker parsing for > 4 GB files
turbojpeg: fix the OS X 64-bit library
Fix isThisType implementation

Previously, the NDPI reader would pick up any TIFF file not picked up by
a reader that was earlier on the list.
Fix findbugs warning
Remove UNSIGNED build logic

Previously for supporting webstart, all jars were
being first generated as name-UNSIGNED.jar and
then signed to the official name name.jar. Then,
they were being re-signed during the webstart
phase. In order to speed up the job and reduce
disk usage (for travis) this logic has now been
removed.
Make 'test' of /specification a no-op

Apparently, there are no longer any unit
test classes in this component so that the
top-level "test-unit" target was failling.

A better strategy is likely to put true
unit-test like activities (schema validation,
etc.) into this target.
FileHandleTest: ignore the turbojpeg library
Recompile turbojpeg jar for Java 1.5
Revert "TIFF: further restrict the usage of YCbCr correction"

This reverts commit 96855558e0da2c07281353ef8c4049b61eb7302a.
turbojpeg: use no-op version of TJLoader
Use a 1.5-safe IOException constructor