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#1

Based on suggestions I've seen elsewhere, and the development workflow we need to follow (multiple developers using the same server, and I don't want them all to masquerade as aegir all the time just to get anything done)

I think that - seeing as the group is :aegir anyway, and the prevailing wisdom is to "join the aegir group" then we should have group write permissions on by default.

All cases of

drwxr-xr-x  aegir:aegir
-rw-r--r--  aegir:aegir

should be changed to

drwxrwxr-x  aegir:aegir
-rw-rw-r--  aegir:aegir

#2

The problem of setting up a non drupal vhost file is a very common issue that involves many later consequences. Just like you mentioned that you were not able to pick up in directory it also involves many similar issues.

#3

The problem of setting up a non drupal vhost file is a very common issue that involves many later consequences. Just like you mentioned that you were not able to pick up in directory it also involves many similar issues.