In the Misc section of the configuration file, you can choose between initializing the database, updating it, or checking the files against the existing database:

ChecksumTest= init|update|check|none

If you use the mode none, you should specify on the command line one of init, update, or check, like: samhain -t check

As of version 1.8.1, there is a new command line flag --interactive to enable interactive updates. If you use this flag together with -t update, you will be asked if the database entry should be updated, whenever samhain encounters a modified file.

As of version 2.8.6, updates can also be done using a text file listing paths (one per line) of files to update, with the command line flag --listfile= path_to_listfile