fix some alien ship trajectory stuff

by request here's a detailed description of the changes in this commit:

it changes some things and makes them better.
rename a variable
gcc fix
fix save deletion from save screen
Overhauled the palette system. Hopefully that's the end of those pesky palette bugs...
Added support for multiple mod folders.
Merge remote-tracking branch 'upstream/master' into chain_notification_windows

Conflicts:
	src/Geoscape/NewPossibleManufactureState.h
	src/Geoscape/NewPossibleResearchState.h