The FlightGear effects framework is documented in $FG_ROOT/Docs/README.effects - the latest version of this file is available here: http://gitorious.org/fg/fgdata/blobs/ma ... ME.effects
FlightGear effects are stored in $FG_ROOT/Effects http://gitorious.org/fg/fgdata/trees/master/Effects
FlightGear shaders are stored in $FG_ROOT/Shaders: http://gitorious.org/fg/fgdata/trees/master/Shaders
Also, the FlightGear wiki contains some more pointers on shader programming: