Greetings Louis!
1. You do not need to have %JAVA_HOME%/jre/lib on your class path. Anything there is automatically on the classpath.
2. You do NOT need to be in your project directory to execute your class files which have been declared to be in a package.
3. You DO need to have the root directory that contains the class files you want to execute on your class path, assuming those classes are in a package. So, if the class file you want to execute is in a package named "com.louiskounios" and that is in a directory named "classes" then set your class path to C:/whateverthepathis/classes or include it on the command line like this:
java -cp "C:/Java Programs/classes" com.louiskounios.<ClassName>
Note that to execute the above my current directory could be C:/someotherdir
If the class you want to execute is not in a package, then
you should not need to specify a classpath, if you are in the same directory that the class file is in. Assuming my current directory is "C:/Java Programs/classes", the command would look lik this:
java <ClassName>
It sounds like you were previously were not putting them in a package which is why you had no problems. Now that you are putting them in a package you need to tell the JRE where to start looking for the package name.
Extra: If the class files you want to execute are in a jar file, then the full path to the jar itself needs to be included on the classpath and then the fully qualified class name. In that scenario, the above command might look like this:
java -cp "C:/whateverthepathis/jarfile.jar" com.louiskounios.<ClassName>
Hope this gets you have the hurdle!