In version 4.0 one can easily trigger an index recalculation from the main 'Repository' section.
In order to manually trigger index recalculation you will need to go to:
[UI] --> [Admin tab] --> [Repositories] --> [Choose the type of repository you are looking for (Local, Remote, or Virtual)] --> [Click on the relevant repository's "Replay" button on the 'Recalculate Index' column].