For Unix shell script and Windows command line you can run the following:
1/For the whole file system on the Repertoire Server:
curl -X POST --basic -u admin:sa http://localhost:8080/repository?action=refresh
2/For a specific file system on the Repertoire Server:
curl -X POST --basic -u admin:sa http://localhost:8080/repository/ElixirSamples?action=refresh
Based on the above your side needs to change the '-u' parameter values to reflect your own login credentials as well as the URL of your Repertoire Server and respective file system. Do note that you will need to install the cURL client for both Unix and Windows to be able to execute the above command. More info on the cURL client can be found here:
Please be mindful that the file system should not be refreshed while the Repertoire Server is receiving requests to generate reports as this will impact performance.