Use faster shift when possible

Optimization for the case where input and output sampling intervals are
equal.
Updated to JOGL 2.1.5

Old version was broken by Java 7 updates.
GLCanvas was incorrectly initialized using Swing on Macs.
Problem seems to have been fixed with JOGL 2.1.5.

Also changed the implementation of paintToFile,
because the JOGL class Screenshot is deprecated.
Restore class SincInterp, now deprecated.

At the time of this commit, the deprecated class SincInterp is
identical to the class SincInterpolator. This copy gives users time to
change all uses of SincInterp to SincInterpolator, before SincInterp is
finally deleted.
Fix documentation
Improve mode switching

More completely disable modes when set inactive.
New methods.
Support irregular arrays of alignment errors.
New method.
Cleanup.
Use latest version of gradle.
Merge remote-tracking branch 'upstream/master'