Deprecate --command-timeout server arg

lib/parser.js

@@ -259,16 +259,6 @@ const args = [
     help: 'Bypass Appium\'s checks to ensure we can read/write necessary files',
   }],
 
-  [['--command-timeout'], {
-    defaultValue: 60,
-    dest: 'defaultCommandTimeout',
-    type: 'int',
-    required: false,
-    help: 'The default command timeout for the server to use for all ' +
-          'sessions (in seconds and should be less than 2147483). ' +
-          'Will still be overridden by newCommandTimeout cap',
-  }],
-
   [['--strict-caps'], {
     defaultValue: false,
     dest: 'enforceStrictCaps',
@@ -356,6 +346,16 @@ const args = [
 ];
 
 const deprecatedArgs = [
+  [['--command-timeout'], {
+    defaultValue: 60,
+    dest: 'defaultCommandTimeout',
+    type: 'int',
+    required: false,
+    help: '[DEPRECATED] No effect. This used to be the default command ' +
+          'timeout for the server to use for all sessions (in seconds and ' +
+          'should be less than 2147483). Use newCommandTimeout cap instead'
+  }],
+
   [['-k', '--keep-artifacts'], {
     defaultValue: false,
     dest: 'keepArtifacts',