Altered run script as it didn't actually work.

Problems were:
- didn't close previous window (issue is that custom title did not remain as "${TERMINAL_ID}" but would change to "rake" when rake executed, so the window would never be found or closed.
- sometimes didn't run rake, but simply ran the following and did nothing else:
	alias quit='' && cd \"${PROJECT_DIR}\" && clear

This commit not perfect (not skilled at osascript) but now works.

Problems:
- will close every rake instance running in Terminal.app