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In NB 6.7 Milestone 2, I verified this on 2 machines (both WinXP, NB6.7M2) one machine using JDK 1.6.0.10, the other 1.6.0.12.... I open a Java source file from a Java SE library project in the editor, select several breakpoints. I execute debug and the class main method is entered and stops on the first breakpoint, which happens to be: System.out.println("Main running "); I press F7 (Step Into) and a new tab immediately opens in the Source Editor for the PrintStream read-only file showing the println method, even though there's no breakpoints set in it. I realize this sounds like what Step Into should do, but in past versions of NetBeans core Java libraries were skipped. To verify I opened the same file from the same project in NB6.5 and perform the exact sequence of steps. When the breakpoint is reached at this line: System.out.println("Main running "); ... it stops. I press F7 and it proceeds to the very next line of code (it does not open any read-only versions of JDK source files. Based on the previous behavior of NB6.5, I think this is a bug, at least P2 or P1. Please correct me if I'm an idiot and this is intended/fixed functionality. Note - I did not mess with any of the new Java Debugger settings in the Options window - this occurs fresh out of the box.
This has changed in 6.7. In fact, many people were very unhappy about the original behavior that step into does not go into JDK sources by default. When they actually want to step into, debugger stepped over instead. We finally decided to change that, because we believe that it's the correct behavior to step into when the user wants that. To get rid of the unwanted side-effects (stepping through class loading, etc.) we've introduced stepping filters. See http://wiki.netbeans.org/DebuggerSources67 and http://wiki.netbeans.org/DebuggerOptions67#section-DebuggerOptions67-OptionsPanelForStepFiltersCategory for details.
Verified ... and Closing all issues resolved into NetBeans 6.7 and earlier.