tools/run-tests.py: A few timeout-related fixes

test/mjsunit/testcfg.py

Index: test/mjsunit/testcfg.py
diff --git a/test/mjsunit/testcfg.py b/test/mjsunit/testcfg.py
index 21139562e7bf539c64464f8180553a6e55279243..c8b972c12f973e2425b3529a51bb615da44cfd45 100644
--- a/test/mjsunit/testcfg.py
+++ b/test/mjsunit/testcfg.py
@@ -57,11 +57,10 @@ class MjsunitTestSuite(testsuite.TestSuite):
 
   def GetFlagsForTestCase(self, testcase, context):
     source = self.GetSourceForTest(testcase)
-    flags = []
+    flags = [] + context.mode_flags
     flags_match = re.findall(FLAGS_PATTERN, source)
     for match in flags_match:
       flags += match.strip().split()
-    flags += context.mode_flags
 
     files_list = []  # List of file names to append to command arguments.
     files_match = FILES_PATTERN.search(source);