#1070: Set default value for output as DOF
#1056: Specify which switches are mandatory
Make directory choice explicit to fix build broken by change in default
#1117: Clean up/update batch processing docs
#1053: Updated docs re: multiple pipelines
#1117: Clean up/update batch processing docs
#1053: Updated docs re: multiple pipelines
issue #1138 - only display first 3 color planes of stacked output image
Merge branch 'master' of github.com:CellProfiler/CellProfiler
issue #1139 always put ImageNumber in image.csv
Added FlowSight / imagestream bioformats reader + updated bioformats class list manually + a couple tweaks because it doesn't populate the plane data
Set a flag in FlowSightReader to make it run a little faster + dogfooding reveals bugs in input modules.
#1143: Corrected split/merge count feature names
issue #1142 ExportToDatabase - fixed bug handling metadata in custom directory name w/o custom file names + test
Merge branch 'master' of github.com:CellProfiler/CellProfiler into release_2.1.1
Undoing inadvertent inclusion of ilastik_pixel_classification.py: Revert "more docu changes"

This reverts commit 2128a354cf73a5e82ed3a749bf6327d1fa43fede.
Undoing inadvertent inclusion of ilastik_pixel_classification: Revert "updated documentation"

This reverts commit 7deaee40542f26343057fd26775f5187049b91cb.
Revert "added initial (and working) ilastik 1.0 classify pixels module"

This reverts commit 516510d952040cf21fe6abedf39374ee23446f18.