This little example gives you a good "JavaDOS IDE" folder structure.
Follow this principal and your project is a huge success :-)
It is very easy to try various JDK versions while developing and testing a java application. All you have to do is give a full path when running java.exe, javac.exe or jar.exe files. Or you may do it like I do and use setenv.bat to update PATH env variable accordingly.
Use given javadosproject.zip as an example when creating your next
java project's folder structure. If you use Java IDEs you still should
follow the same principal, althought IDE will handle compilations and running an app.
List of Java IDEs can be found here.
Always create a MANIFEST.MF file and provide name and version info. Note that, NEWLINE is mandatory after last name=value pair. This is just a quality of service to include it to application jar file. See compile.bat and jar.bat how I do it in pure DOS projects.
If you use JavaIDE then most tasks are automated even more, but its still good to know how things go in a lowest model IDE.