In the ./makee/ top level directory there are two parameter files, "makee.HIRES.param" and "makee.ESI.param". These files contain parameters in addition to those specified on the command line. These parameters control such things as polynomial fitting, object width fraction, and cosmic ray rejection thresholds.
Usually you do not want to change these values, however, in cases where MAKEE fails it may be possible to achieve some adequate results by changing some of these values.
These files are read at run-time, so there is no need to re-compile if you change the values. Read the descriptions in the files for more information.