(Yep, still on 609, but this bug looks pretty obscure.)

If you set a breakpoint and then remove the source directory where the
breakpoint
is set, when you save the project, an error dialog appears saying that the
project can't be saved.

Workaround: before saving, go to Run->View Breakpoints and remove the
breakpoint manually.

Here is the stack trace:

java.lang.NullPointerException
        at com.intellij.debugger.breakpoints.f.run(f.java:1)
        at com.intellij.psi.impl.n.run(n.java:5)
        at com.intellij.vfs.VirtualFileManager.a(VirtualFileManager.java:54)
        at com.intellij.psi.impl.v.b(v.java:239)
        at com.intellij.debugger.breakpoints.a.b(a.java:446)
        at com.intellij.debugger.a.c.b(c.java:74)
        at com.intellij.project.a.b.a(b.java:160)
        at com.intellij.project.a.b.f(b.java:132)
        at com.intellij.project.a.e.a(e.java:17)
        at com.intellij.ide.util.s.c(s.java:8)
        at com.intellij.project.a.e.c(e.java:4)
        at com.intellij.ide.impl.bc.run(bc.java)
        at com.intellij.command.a.b.a(b.java:0)
        at com.intellij.ide.impl.p.d(p.java:0)
        at
com.intellij.ide.actions.CloseProjectAction.actionPerformed(CloseProjectActi
on.java:6)
        at com.intellij.openapi.actionSystem.impl.j.run(j.java:1)
        at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:154)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:337)
        at com.intellij.ide.c.dispatchEvent(c.java:1)
        at
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.ja
va:131)
        at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java
:98)
        at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
        at java.awt.EventDispatchThread.run(EventDispatchThread.java:85)

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