The "delete" command:

Usage: fossil rm FILE1 ?FILE2 ...?
   or: fossil delete FILE1 ?FILE2 ...?

Remove one or more files or directories from the repository.

This command does NOT remove the files from disk.  It just marks the
files as no longer being part of the project.  In other words, future
changes to the named files will not be versioned.

See also: addremove, add