Java APIs

Hi All ,Hope it would be little confusing I unzipped 7 jar files in a folder ..for ex, C:/src/actualcode where actualcode contains 7 jar files ,i unzipped and decompiled the class files using jd compiler and then saved the files using jar resources and finally got all java files..now with the zipped files inside the actual code folder ..(instead of jar files) i converted the zipped files in to a folder and tried running the tool and got an error saying "No connector specified error".This tool is related to Peoplesoft Integration Gateway plugin using Java.Then i decided to compile all the java files again and convert it to class files and then jar it so tat finally it should reflect as it was like in previous manner.I did not modify the code but when i tried to compile java files it is throwing so many errors.I could compile some java files and not the remaining.Also Each folder contains so many java files how to compile all the java files inside a folder.Is there any specific command..also What am trying to do (Reverse Engineering procss) is tat meaning ful..will it work.once after compiling all the java files...Please Advice...Guide me in the correct path...