I'm looking for interesting ways to use my FPGAs (Altera DE2 and DE2-115) and it seems that uClinux includes some files for DE2-115 in its distribution but there is no documentation how to use it. What is the use of the files in the DE2-115 directory if not for running Linux on the DE2-115?
Yes that should be possible and is indeed the purpose of the files in that directory. Johan Granath from the AGSTU School of Higher Vocational Education has a good PDF document describing how to achieve it in detail that includes a simple custom hardware kernel module:
Along similar lines is a publication by David Lariviere and Stephen A. Edwards from Columbia University: