Keep owned references to builtins module, "cython_runtime" module and...

Keep owned references to builtins module, "cython_runtime" module and preimport module to prevent crashes when they get removed from sys.modules. Generate cleanup code for them in the end.
Closes #2885.

Cython/Compiler/ModuleNode.py

@@ -2704,11 +2704,11 @@ class ModuleNode(Nodes.Node, Nodes.BlockNode):
 #            if entry.type.is_pyobject and entry.used:
 #                code.putln("Py_DECREF(%s); %s = 0;" % (
 #                    code.entry_as_pyobject(entry), entry.cname))
-        code.putln('#if CYTHON_COMPILING_IN_PYPY')
-        code.putln('Py_CLEAR(%s);' % Naming.builtins_cname)
-        code.putln('#endif')
-        code.put_decref_clear(env.module_dict_cname, py_object_type,
-                              nanny=False, clear_before_decref=True)
+        if Options.pre_import is not None:
+            code.put_decref_clear(Naming.preimport_cname, py_object_type,
+                                  nanny=False, clear_before_decref=True)
+        for cname in [Naming.cython_runtime_cname, env.module_dict_cname, Naming.builtins_cname]:
+            code.put_decref_clear(cname, py_object_type, nanny=False, clear_before_decref=True)
 
     def generate_main_method(self, env, code):
         module_is_main = "%s%s" % (Naming.module_is_main, self.full_module_name.replace('.', '__'))
@@ -2815,13 +2815,12 @@ class ModuleNode(Nodes.Node, Nodes.BlockNode):
             '%s = PyImport_AddModule(__Pyx_BUILTIN_MODULE_NAME); %s' % (
                 Naming.builtins_cname,
                 code.error_goto_if_null(Naming.builtins_cname, self.pos)))
+        code.put_incref(Naming.builtins_cname, py_object_type, nanny=False)
         code.putln(
             '%s = PyImport_AddModule((char *) "cython_runtime"); %s' % (
                 Naming.cython_runtime_cname,
                 code.error_goto_if_null(Naming.cython_runtime_cname, self.pos)))
-        code.putln('#if CYTHON_COMPILING_IN_PYPY')
-        code.putln('Py_INCREF(%s);' % Naming.builtins_cname)
-        code.putln('#endif')
+        code.put_incref(Naming.cython_runtime_cname, py_object_type, nanny=False)
         code.putln(
             'if (PyObject_SetAttrString(%s, "__builtins__", %s) < 0) %s;' % (
                 env.module_cname,
@@ -2833,6 +2832,7 @@ class ModuleNode(Nodes.Node, Nodes.BlockNode):
                     Naming.preimport_cname,
                     Options.pre_import,
                     code.error_goto_if_null(Naming.preimport_cname, self.pos)))
+            code.put_incref(Naming.preimport_cname, py_object_type, nanny=False)
 
     def generate_global_init_code(self, env, code):
         # Generate code to initialise global PyObject *