Creating Packages and then adding them to a Zip File...

I have a two part question.
I know how to create a package by using the "package" statement.
My question is can you keep .java code in its own file system(directory) and compile it so the resulting package is put into a common directory?  

I am trying to create packages and have them put into a common file system.  The only way i know how to do this is by putting the .java code into this common directory and compile it.

The reason for this is so i can zip all the classes and add them to one common class directory.

My second question is:  
Does anyone have an example of a makefile that will compile .java code then put it into a .zip file?

thanks in advance!!!!!!!!!!!!!