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I always have to navigate to the Qsys Project path for re-generating Qsys.
Is there a way to set the Qsys path? I want to open Qsys from my Quartus and Qsys jumps to its project path.
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I noticed this too, and did not find a work-around as far as using the GUI goes. However, you can use a Tcl script to see if the .qsys file has changed, and then use Tcl to re-run the "Generate" stage.
Take a look at the DE0-nano SDRAM project I posted, and look at the synth.tcl and synth_qsys.tcl files.
http://www.alteraforum.com/forum/showthread.php?t=45927 Note that this project also turns the .qsys file into a .tcl file, but you can skip that step if you like.
Cheers,
Dave