Fossil does not use the manifest or manifest.uuid files.  Those files
are created purely for the convenience of the application.

For example, the source code to fossil itself (which is stored as a fossil
repository) looks at the manifest and manifest.uuid files to get the date
and time and version information that is displayed when you type:
"fossil version".  And SQLite gets the information returned by the
sqlite3_sourceid() function in the same way.