Fixed a bug with node placement after merge

If the user attempted to merge two branches of uneven length, the
resulting merge node was placed incorrectly.
rules for skyscrapers added
Made checkboxes for Proof menu checked by default (with Avi's help).
Made the Proof menu's checkboxes update the state on initialization (tested, wasn't happening properly before).
Popups now occur when an exception is thrown. Fixes issue #53.
Arrows pointing to collapsed nodes are straight
Collapsed nodes are lined up horizontally instead of vertically.
Fixed a few more quirks with collapsed nodes.
Collapsed nodes are now drawn at the average x-position of the adjacent nodes.
Updated Basic rule names in skyscrapers powerpoint.
Added getters for the menu item's states (checkboxes), eliminating some potential for error (and providing a way to access the default application flag at all from outside the LEGUP_Gui class (which wasn't previously possible)).
Set useDefault in JustificationPanel.actionPerformed based on the menu option for allowing default rule application.
Clicking on a transition now causes the relevant rule to be selected in the relevant JustificationPanel on the left. Closes issue #51.
Fixed many compile warnings
Merge branch 'master' of github.com:Bram28/LEGUP
Added Ripple Effect Rules
Fixed all remaining compile warnings
Merge branch 'master' of github.com:Bram28/LEGUP
Commented out initial prompt for a puzzle.
added bugged proof