Fix #6281 - Make sure puppetdoc analyzes all files

It can happen that when parsing a file puppet parses other manifests
if they get imported (this is at least true for site.pp, even in
ignoreimport=true). Thus those files are now "watched".
But puppetdoc needs to analyze all files, and since 99c101 we are now
checking if the file was already parsed to not reparse it again.
If that was the case, though, we weren't analyzing the produced code.
Thus it was possible to not produce documentation for the site.pp content.

Signed-off-by: Brice Figureau <brice-puppet@daysofwonder.com>