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I'm posting this here, so when I run into this problem again in the future I can just Google the solution.
By default, Quartus 13.1 doesn't support using EPCS32, or the equivalent M25P32, flash parts but if you put the following line in a quartus.ini file you can re-enable support for the part.pgm_allow_epcs32=on
The best place for the quartus.ini file is the same directory you're running quartus from when you convert the .sof file to a .jic. This will allow you to select the EPCS32 part in the Convert Programming File dialog. For the programmer on a Windows PC, you'll probably need to put it in the same directory as the quartus_pgmw.exe file you're runnning (either in bin/ or bin64/). Thanks to stu84 in this post (http://www.alteraforum.com/forum/showthread.php?t=27520&p=110133#post110133) for the ini line.
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