When first run, SiberMerge creates two files, .ccm_merge.enc and .ccm_merge.dat.
The file named .ccm_merge.enc is located in your (UNIX) home or (Windows) profile directory and contains a list of file encodings that are offered in the encoding menus. Initially, the list includes all supported encodings; you can shorten the menus by deleting encodings that you do not use.
The file named .ccm_merge.dat is located in your (UNIX) home or (Windows) profile directory and contains the set of default merge options, such as whether or not to ignore spaces, etc. You can edit this file to modify your default merge options.