Hi,
QSF Files mean "Quartus Setting File" and they are TCL (Tool Command Language) scripts :
usualy, All lines begin with a command follow by arguments BUT you may have substitutions of command (enclosed by square brackets) and variable (character '$' and name of variable).
A line that begins by a '#' is a comment BUT be careful about brackets even in comments (common newbie error).
QSF are written in very simple TCL (no nested command, no procedures...)
TCL is case sensitive !
1. I don't think there is an order but it could be. See Quartus scripting in
www.altera.com 2. there are a few commands that are ignored (backward compatibility, or simply useless commands) (Maybe I misunderstood your question)
3. there is an order on the files read by Quartus software. See Quartus scripting in
www.altera.com or in help (quite ugly to search)