databases/mongodb60: update to 6.0.6

trivial version bump
one patchfiles is included in the source now
poudriere stage-qa: ok

Changes:
https://www.mongodb.com/docs/manual/release-notes/6.0/#6.0.6---may-12--2023

Please read the release notes: Some past releases have critical issues.

Followed an upstream change in mongod.conf about removal of 2 settings. See
UPDATING 20230416.