LNMail is shipped with a migration tool. It is used to categorize existing mail messages on the server as well as in archives. Therefore it loops over all mail messages and adds categories to it according to the directory they are stored.
If for example a message is stored in the Lotus Notes directory "/Projects/LNMail", the migration tool adds the categories "Projects" and "LNMail" to this message. The messages itself are not moved or otherwise touched. Only the categories are added, so you will also find them in the Lotus Notes client, where it was before.
With the newly added categories, it is later possible to easily build up different views in LNMail. Like that a view "Projects" can be created, where all messages are displayed, which are placed anywhere below the "Projects" directory. So, not only messages in "LNMail", but all other subdirectories are shown, since they all include the "Projects" category.
It is also possible to build up the same structure as in the original Lotus Notes client. Simply create the same directory structure and create a view "/Projects/LNMail", where only mail messages are shown, which include the categories "Projects" as well as "LNMail".