Backport PR #575 on branch 3.x (PR: Fix debugger stop in breakpoints set on modules if stop on first line option is disabled) (#578)

Author: meeseeksmachine

spyder_kernels/customize/spyderpdb.py

@@ -287,6 +287,7 @@ def stop_here(self, frame):
         if self.stopframe == self.botframe and self.stoplineno == -1:
             return False
         if self.continue_if_has_breakpoints and self.should_continue(frame):
+            self._wait_for_mainpyfile = False
             self.set_continue()
             return False
         if (