The latest version of the Papilio Loader now works under Linux.
To compile libftdi-dev package must be installed. In directory Papilio-Loader-Papilio-Loader-V2.4/papilio-prog type
$ sh autogen.sh $ ./configure $ make
This will create papilio-prog binary which can be executed from that directory and should show something similar to this
$ ./papilio-prog -c Using built-in device list JTAG chainpos: 0 Device IDCODE = 0x24001093 Desc: XC6SLX9 ISC_Done = 1 ISC_Enabled = 0 House Cleaning = 1 DONE = 1