Merge pull request #1001 from qidane/new-time

New time docs and samples
Merge pull request #985 from qidane/transform-catalog

Updating transform catalog for 2013-10-dev-1
Location: only delegate to File.isHidden() on Windows

This bypasses substantial performance problems when calling isHidden()
on Mac OS X/Linux over NFS.  Fixes #6586, see #12027.
FormatReader: speed up getUsedFiles()

We can assume that each call to getSeriesUsedFiles(...) will contain an
array with no duplicates.  If there is only one series in the fileset,
then, we can speed up large filesets by removing the extra check for
duplicate files.

See #12027.
DICOM: ensure that getSeriesUsedFiles returns an array of unique paths
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 990 (Memoization fixes (rebased onto develop))
merge develop -D org: PR 991 (Only add a MetadataOnly element if no TiffData elements are present)
merge develop -D org: PR 999 (Fix for single channel  meas_mode 13 data (rebased onto develop))
merge develop -D org: PR 1004 (Update docs regarding BF and Eclipse (see #12127). (rebased onto develop))
merge develop -D org: PR 1005 (ND2: always set the field index to 2 (rebased onto develop))
merge develop -D org: PR 1006 (Read internal pyramids from CellSens .vsi data (rebased onto develop))
merge develop -D org: PR 1007 (SVS import and TIFF export fixes (rebased onto develop))
merge develop -D org: PR 1008 (Enable SDT plane preloading by default (rebased onto develop))
merge develop -D org: PR 1014 (Add initial structure for decompressing JPEG XR images (assist #8493).)
merge develop -D org: PR 1027 (C++: Add cmake build infrastructure for libtiff and threading)
merge develop -D org: PR 1028 (Large fileset performance improvements (rebased onto develop))