Debugging and stepping through breakpoints stopped working

I don't know why I can no longer step through the breakpoints I have set. Last time I tried this a few weeks ago with a project, I could step through a program running in debug mode.

I made sure I am breakpointing the right source and that my breakpoints are not being "muted".

JDK 1.5
IDEA 5.1.2
on linux using Gnome.

help

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apparently ]]> has to come before JDK libraries in the Modules' "Order/Export" tab of project settings.

that seemed to fix it, although I don't know why this is.

if anyone knows please comment.

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