[cmd] Override --config file options from command line

With this change options specified on the command line after the --config option
will override options specified in the config file.

analyzer/tests/functional/config/test_config.py

@@ -59,7 +59,7 @@ def setUp(self):
                   encoding="utf-8", errors="ignore") as source:
             source.write(simple_file_content)
 
-    def __run_analyze(self):
+    def __run_analyze(self, extra_options=None):
         """
         Run the CodeChecker analyze command with a configuration file.
         """
@@ -68,6 +68,9 @@ def __run_analyze(self):
                        "-o", self.reports_dir,
                        "--config", self.config_file]
 
+        if extra_options:
+            analyze_cmd.extend(extra_options)
+
         # Run analyze.
         process = subprocess.Popen(
             analyze_cmd,
@@ -94,6 +97,23 @@ def test_only_clangsa_config(self):
         self.assertIn("clangsa analyzed simple.cpp", out)
         self.assertNotIn("clang-tidy analyzed simple.cpp", out)
 
+    def test_override_config_file(self):
+        """
+        Run analyze command with a config file which enables the clang-tidy
+        analyzer only and override this option from the command line and enable
+        only clangsa analyze.
+        """
+        with open(self.config_file, 'w+',
+                  encoding="utf-8", errors="ignore") as config_f:
+            json.dump({
+                'analyzer': ['--analyzers', 'clang-tidy']}, config_f)
+
+        out, returncode = self.__run_analyze(['--analyzers', 'clangsa'])
+
+        self.assertEqual(returncode, 0)
+        self.assertIn("clangsa analyzed simple.cpp", out)
+        self.assertNotIn("clang-tidy analyzed simple.cpp", out)
+
     def test_empty_config(self):
         """
         Run analyze with an empty config file.

bin/CodeChecker.py

@@ -123,7 +123,11 @@ def signal_handler(signum, frame):
         if 'func_process_config_file' in args:
             cfg_args = args.func_process_config_file(args)
             if cfg_args:
-                sys.argv.extend(cfg_args)
+                # Replace --config option with the options inside the config
+                # file.
+                cfg_idx = sys.argv.index("--config")
+                sys.argv = sys.argv[:cfg_idx] + cfg_args + \
+                    sys.argv[cfg_idx + 2:]
                 args = parser.parse_args()
 
         try: