Added vim modelines and license headers to most of the files

GatingSet query moved from OpenCytoVisualization to OpenCytoPreprocessing, since it will also be used in OpenCytoQualityControl

OpenCytoPreprocessing.r :
- hash value does not use the study variables anymore, but does use the set of selected files
- all study variables are written into the gating set file

opencyto_preprocessing-0.00-0.01.sql and opencyto_preprocessing.xml : modified to not include the study variables field anymore

begin.view.xml : CheckBoxMemory.js plug in dependency added so that the selected rows in a grid table are remembered across query() refreshes

ExtendedLovCombo.js : getCheckedArrayInds() method added that returns the array of indices of checked items

OpenCyto.css : z-index for infoMask and x-mask-loading-custom classes decreased not to interfere with others

OpenCyto.js :
- captureEvents() modified a tad to be more informative
- timeout value fixed to be 1 hour (backend Ajax changed from using Ext3 to Ext4, so this is reflected)
- remove() method added to array's prototype that can be used to remove by values

OpenCytoPreprocessing.js :
- selected study variables are 'cached' so that no query is done if a panel card is changed, but the selection of the study variables has not changed from last time
- notSorting flag added to select all of the files only when the store's contents have changed (and not when they have been simply sorted)
- getAllValuesAsArray() method added to an instance of the SuperBoxSelect
- files string is now passed to the back-end R script containing the set of the subselected files be part of the gating set
- RowNumberer() added to the grid table
- CheckBoxMemory plug is added so that the selected rows in a grid table are remembered across query() refreshes
- LABKEY.QueryKey.encodePart() had to be used in order for LabKey to properly understand the data
- navHandler() modified slightly so that the grid table is loaded only when going from page 1 to page 2