Read usercode & checksum of FPGA using TCL command

You've probably already figured this out by now, but posting for the benefit of future searches.

There's a command line executable quartus_stp, which includes a jtag package with a bunch of tcl commands. It's documented in the following.

http://www.altera.com/literature/manual/tclscriptrefmnl.pdf?gsa_pos=1&wt.oss_r=1&wt.oss=quartus tcl scripting reference manual

you can use two commands to shift in IR values and DR values as needed.

The IR value for most Altera devices is x007 (10 bits)

An alternate way to shift it out is to use the JTAG debugger.