populate_documentation: remove support for root items

They are a relic from the time when we used svn modules.

Nowadays extraction settings are per-repository and they
can be listed explicitly.

The only remaining user (calligra) has been ported from
root to a series of entry.

Moreover, less code will make it easy to make
populate_documentation use the repository information
from get_paths (basically needed after the migration
to the new structure).