How to read flash using nios2-flash-programmer?

The flash programmer doesn't program/configure the FPGA. To do so (if you think about it), would be rather difficult, if not impossible. There is no common, hard-coded flash interface on an FPGA... It's all soft IP that is programmed at configuration time, or via the Quartus II programmer. Additionally, the flash programmer uses the same "jtag conduit" code as the QII programmer, so, if you can't use the QII programmer, you're not going to be able to use the flash programmer. There is a nios2-configure-sof command, but it is just a thin wrapper around the QII programmer.

You should, however, be able to install a subset of Quartus II only for programming the device.... ("basically" the jtag-related DLLs or SOs from a QII installation) If you've used the flash programmer (at all), you already have this subset. Try typing "jtagconfig -n", when connected to a board with a configured FPGA and you should see some useful information. Something like the following:

1) USB-Blaster 
  020B40DD   EP2C35
    Node 11104600
    Node 0C006E00

In the above case, the first line represents the jtag conduit medium (in this case a USB Blaster), the second line represents the type of device I'm connected to (a 2C35), and the other two lines represent the CPU's jtag debug module and the jtag_uart. Think of Altera's on-FPGA JTAG implementation as a "hub" with many possible nodes. [jtag_uart, jtag_debug, Signaltap, etc.]

Cheers,

- slacker