The AUTO input files are now called c.xxx (the constants file), and h.xxx (the HomCont constants file, only used with HomCont); the output files are called b.xxx (the bifurcation-diagram-file), s.xxx (the solution-file), and d.xxx (the diagnostics-file). There are also minor changes in the formatting of these files compared to recent versions of AUTO, such as AUTO97 and AUTO2000. The main change compared to AUTO97 is that there is now a programmable Python CLUI.
When upgrading from AUTO2000, you can continue to use equations-files written in C. However, there is now a strict difference between indexing of the array par[] in the C file and the references to it using PAR() in constants files and output, using par[i]=PAR(I+1). In practise this means that you do not have to change the C file, but need to add 1 to all parameter indices in the constant files, namely ICP(I), THL(I), and UZR(I). For example, the period is referenced by par[10] in the C file, but by PAR(11) in the constants file. Equation files written in C are used in the homoclinic branch switching demo in Chapter 27.