FIX: add in connectedApps, quickActions and fix staticResources.
FIX: ensure that copyFilesToPackage works correctly if there are multiple periods in the name (such as with quick actions)
FIX: ensure that packageLists ignore lines that start with a hash (as it means it should be escaped/ignored.
FIX: allow the removeExtension to know the folder name of the file to be removed because the way SalesForce handles quickActions isn't very well thought out.