Update .gitignore

Adding recommended exclusions, as per https://help.github.com/articles/ignoring-files#global-gitignore
Fixed bug in Stored Characters numberSelected
Added toggle in RecAncStates to return only selected characters, if the
character source is selectionable
Merge pull request #1 from wmaddisn/master

StoredCharacters fix & Selected Only in TraceCharacter
Fixed inclusion/exclusion of characters from within the data editor so
that it would work if the whole column was selected in any way
(including just having all the cells for that character for all taxa
selected).
Merge pull request #4 from wmaddisn/master

Inclusion/exclusion of characters from within the data editor now works if the whole column was selected in any way
Altered code of Query integer dialog boxes to allow display of a
secondary message below the entry field for the integer.
Adjusted Fixed Taxon Spacing so that one could reset to default spacing
by entering a value of 0.
Cleaned up SquareLinetree so that tracing of characters had fewer odd
positions of lines and boxes.
More cleanup on SquareLineTree trace character display.
More adjustments of SquareLineTree to deal with equivocal nodes in trace
characters.
Starting to add disconnectability to tree search
Small fixes to Rec anc states, align
Minor to ShellScriptRunner
First major steps to disconnectibility of external tree inference
Fix to fileExists
New date string util
fix encoding problems with StringUtil source
Fixed bad high-ASCII characters in StringUtil
Yet another attempt as fixing the high-ascii stuff.  Switched workspace
to UTF-8 as default.
Fixes to MesquiteFile to avoid //
Further fixes to improve disconnectability of external tree searches
Updated the build number!
Ignore IntelliJ files