Update README.md

Author: soerenarlt

README.md

@@ -18,16 +18,16 @@ To run one of the included examples, type e.g.
 pytheus run --example ghz_346
 ```
 
-To list all examples, type
+NOTE: currently there is an issue in some installations where examples are not by the above command. You can also run config json files by referring to them by their path in the package resources. they can be found in the directory `pytheus/graphs`
 
 ```
-pytheus list
+pytheus run PATH_TO_YOUR_INPUT_FILE
 ```
 
-To run your own input file, type
+To list all examples, type
 
 ```
-pytheus run PATH_TO_YOUR_INPUT_FILE
+pytheus list
 ```
 
 Output of optimization is saved to a directory called `output`. Names of the subdirectories are specified by the name