Merge pull request #1 from wmaddisn/master

StoredCharacters fix & Selected Only in TraceCharacter
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
Merge pull request #8 from wmaddisn/wayne2013.12.14

Wayne2013.12.14
Revert "Merge pull request #8 from wmaddisn/wayne2013.12.14"

This reverts commit 48925be6dbf5529d865d47b1b075760ba813fe58, reversing
changes made to a4cca9d44d5673b512f4a35d549334f760fdf462.
Adding choice to filter trees either that satisfy or fail the criterion
Enabling reading of translation table with default names t0, t1 etc
Enabling t0,t1 taxon names in tree reading
Adding missing data colouring to terminals and clades with missing data.
Reinterpreting Balls & Stick terminal spots as refering to observations
Enabling findTerminalBox so that trace character could inform user of
observed states for terminal boxes
Also for both terminal boxes and terminal branches, show BOTH observed
and reconstructed states
Icons and titles change in window tabs
Adding icons to window tabs
Shorter and more informative window tab names
More refinements to icons in window tabs
Merge pull request #9 from wmaddisn/wayne2013.12.15

Wayne2013.12.15
Merge branch 'master' of https://github.com/MesquiteProject/MesquiteCore
into MesquiteProject-master

Conflicts:
	Source/mesquite/align/MAFFTAlign/MAFFTAlign.java
	Source/mesquite/lib/MesquiteModule.java