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Breakpoint management is accomplished in the Breakpoints view which is available in the Debugging perspective, by default. It’s typically the first tab in the upper-right view area. You can then use a shift-click to select all breakpoints and clear them.
And maybe you suffer an exception which is catched later on. If the exception or any super class of it is marked to stop execution, it will cause the debugger to stop at the line the exception occures. So maybe rechecking the exception list of the debugger may also help.
I found the problem. I had a break point in a another file but I was getting stopped at a different place. I am not able to recreate the problem. I think my system was in some weird state.