Volume Viewer: move classes to non-default package

The reason is that classes in the default package take silent precedence
over classes made available via wildcard imports, which has caused
confusion on multiple occasions.

For example, the statement "import java.awt.*;" does *not* import the
java.awt.TextField class when a packageless "TextField" class is also on
the classpath.

See this thread for further rationale and discussion:
https://groups.google.com/d/msg/fiji-devel/6Ua05iccSVo/5ZLrUO-FhmUJ
Reconstruct Reader: Set nonlinear transforms to identity
Reconstruct Reader: Fix Reconstruct transform scale calibration issue upon import
Reconstruct Reader: Suppress unnecessary sysouts, display message for recalibration
Merge pull request #26 from larrylindsey/reconstruct-trakem2

Reconstruct Reader: Support for nonlinear transforms (sort of) and scaled projects
Stitching: add ignore stage Z option

For multi_series_file and grid stitching, this flag, when enabled, will
force all Z stacks to be treated as though their stage position was 0,
effectively aligning them.

This option can help resolve issues stitching datasets that were
acquired in a cascade from an origin point.
Stitching plugin - fusion: report status

The fusion operation of the stitching plugin now displays a status bar for each
block being fused, and reports the overall status (current C, T slice being
fused).
Merge branch 'stitching-status'

Adds status reporting to the stitcher's fusion operations.
Merge branch 'ignore-z-stage'

Adds a flag for grid and multi-series stitching to ignore Z stage coordinates,
aligning everything to 0.
Stitching_: remove timestamp from Eclipse metadata

It is not needed, and Eclipse 4.3 strips it out anyway.
Add more JARs to .gitignore
Trainable Weka Segmentation: include flag to use old color format in the instance creation.
Trainable Weka Segmentation: include flag to use old color format in the array.
Merge branch 'master' into trainable-seg-gui
Trainable Weka Segmentation: added option to use old color format when creating instances in place.
Trainable Weka Segmentation: added method to read the old color format flag.
Trainable Weka Segmentation: added message when using old color format.
Support runs of Vaa3d pbd difference bytes that cross input stream block boundaries.
Stitching_Grid: add default BF settings

When running BF.openImagePlus, always ensure the dimension input order
will match the underlying dataset's order, and the output order will be
XYCZT to match the ImageJ constraints.

Also, ensures crop will be false.
Stitching_Grid: add "TilesToRois" checkbox

When this option is selected, all tiles in the stitched image will be
added as Rois to the RoiManager. Each will be labeled with its
appropriate Z,C,T and imageIndex coordinates in the underlying dataset,
as well as the file name on disk that the tile was read from.