Starting disconnectibility of Garli running
Shift temp files to be beside project home file
Fixes to temp file location beside home file
Working on modifications of GARLI to read in GARLI scores etc. under the
new partly disconnected system
Merge remote-tracking branch 'origin/disconnectability1' into
disconnectability1

Conflicts:
	zephyr/Source/mesquite/zephyr/GarliRunner/GarliRunner.java
Now reads in GARLI scores if disconnected.
Fixing snapshot to recover tree window after reconnect
Merge remote-tracking branch 'origin/disconnectability1' into disconnectability1
useless change to see why push doesn't seem to work
More progress on GARLI disconnections.
Merge remote-tracking branch 'origin/disconnectability1' into disconnectability1
More changes in separating parts of GarliRunner
Rewrote GetTrees in GarliRunner so that it now uses the pieces of the
disconnectible system.
Fixed bootstrapping in GARLI under the new system.
Fixed bug with project panel not being updated after GARLI run.
Warning on file close that run is ongoing
Merge remote-tracking branch 'origin/disconnectability1' into disconnectability1
Switching to ExternalProcessRunner modules from ShellScriptRunner to
permit alternative execution places and styles
Merge pull request #1 from DMaddison/disconnectability1

Disconnectability1 changes merged into master