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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.

Options:
  -K|--keep-rid1     Read the filename of the artifact with RID=1 from the
                     file .rid in DIRECTORY.
  -P|--keep-private  Mark the artifacts listed in the file .private in
                     DIRECTORY as private in the new Fossil repository.

See also: deconstruct, rebuild