You cannot do that.

I think there are some potential approaches:

1. Copy perldb.pl into its own directory, and start a fresh git repository with it.
   This way you get a clean directory but lose all connection to the upstream. It is also easy to set up and understand. Importing changes from upstream will likely devolve into manually resolving diffs between bleadperl and your version.
2. Clone the perl repository and ignore the rest of the files. This way, you can always resynchronize with the changes in Perl, at the cost of also synchronizing a lot of files you don't care about.
3. Clone and then rewrite the perl git directory using git filter-branch to only transfer the history of perl5db.pl into the new repository. This way you keep all the file history of perl5db.pl and you can also periodically get a fresh version of the perl repository and export the perl5db.pl related patches to rebase your changes on it.
4. Speak to p5p to spin off perl5db.pl from the core and make the CPAN version (to be released by you) upstream. This allows development to occur outside of the Perl core and the new perl5db.pl will then be periodically be copied into the perl repository.