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The "reconstruct" command:

Usage: fossil reconstruct ?OPTIONS? FILENAME DIRECTORY

This command studies the artifacts (files) in DIRECTORY and
reconstructs the fossil record from them. It places the new
fossil repository in FILENAME. Subdirectories are read, files
with leading '.' in the filename are ignored.

   -K|--keep-rid1    Read the filename of the artifact with
                     RID=1 from the file .rid in DIRECTORY.

See also: deconstruct, rebuild