If you run the program "sysedit" from Windows, you will get the screen below.  Window considers these 5 files it's `system' files.   The first two, `autoexec.bat' and `config.sys' are DOS files that configure DOS programs when you boot-up your PC.  `Win.ini' and `System.ini' are Windows "Initilization" files that configure certain Windows functions as Windows loads.  `Protocol.ini' is a network thing.  None of there are critical files, but when they contain erroneous commands they can cause startup problems.  I mention this only to forewarn you of bootup error messages - or allow you to troubleshoot certain virus problems which attack these files. 

These files can be edited by simply clicking on them, highlighting the bad command, deleting it, and then saving the file.