In version older than or equal to Java version 5 you must specify each jar individually, and the root of your source, on your classpath e.g.
java -cp a.jar:b.jar:c.jar:./src MainClass
In version 6 you can use wildcards for the jars e.g.
java -cp ./src:* MainClass
but it might be cleaner putting your jars into a sub directory e.g.
java -cp ./src:./jars/* MainClass
So basically, your makefile or start script needs to construct a command like one of the above.
More info - Sun docs (v6)
Update - in response to your second edit, you need to specify the full main class name, so if the class is in a package called 'com.mypackage.MainClass' then you need to do:
java -cp ./src:./jars/* com.mypackage.MainClass
I'd also suggest getting the command working as a standalone command first, before getting the whole script running. By removing moving parts it will be faster to debug and easier to see what's going on.
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