fix: Clear breakpoints before running any script with debugger

IPython/core/magics/execution.py

@@ -849,6 +849,7 b' python-profiler package from non-free.""")'
         bdb.Breakpoint.next = 1
         bdb.Breakpoint.bplist = {}
         bdb.Breakpoint.bpbynumber = [None]
+        deb.clear_all_breaks()
         if bp_line is not None:
             # Set an initial breakpoint to stop execution
             maxtries = 10

IPython/core/tests/test_run.py

@@ -165,8 +165,8 b' def doctest_reset_del():'
 class TestMagicRunPass(tt.TempFileMixin):
 
     def setup(self):
-        """Make a valid python temp file."""
-        self.mktmp('pass\n')
+        content = "a = [1,2,3]\nb = 1"
+        self.mktmp(content)
         
     def run_tmpfile(self):
         _ip = get_ipython()
@@ -213,6 +213,16 b' class TestMagicRunPass(tt.TempFileMixin):'
         with tt.fake_input(['c']):
             _ip.magic('run -d %s' % self.fname)
 
+    def test_run_debug_twice_with_breakpoint(self):
+        """Make a valid python temp file."""
+        _ip = get_ipython()
+        with tt.fake_input(['b 2', 'c', 'c']):
+            _ip.magic('run -d %s' % self.fname)
+
+        with tt.fake_input(['c']):
+            with tt.AssertNotPrints('KeyError'):
+                _ip.magic('run -d %s' % self.fname)
+
 
 class TestMagicRunSimple(tt.TempFileMixin):