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[news.eclipse.newcomer] workspace setup

hello,

i am new to eclipse, and i am a second year Computer Engineering student at Rochester Institute of Technology, and i was hired by my professor to help him get ready for Computer Science 1 class. its been desided this year that all development will be done with eclipse instead of emacs (yay!). The only problem i have so far is trying to setup the directories the way my professor wants. he wants a main CS1 directory, with 3 subdirectories: labs, lec, and proj. from there he wants to be able to have individual projects under each of those directories. my problem is setting up the workspace so that it will do that. i tried to make it all under one big project, however i found out that i cannot have a project within a project. next i tried to just use source folders, however when i went to debug and compile multiple different programs (example: lab1 and lab2), it compiled both of them because they are all under one project. I would like to be able to have it so that i can have the correct directory setup and still be able to compile and run lab2 without having to compile and run lab1, because if the student doesnt have lab1 working, they can still work on lab2 (basically i need them to be independent of each other). is there any way this can happen under one workspace? i apologize if this is a newb question because well, i am new to eclipse myself. thanks for any help!