cli/new: only ignore .notmuch at top level

Since the bug was first reported in [1], notmuch has gained the
ability to have the database located outside the mail root, hence this
this change differs slightly from Jani's proposed solution [2] in not
using notmuch_database_get_path, but rather the already retrieved
mail_root.

[1]: id:87mwhifu9a.fsf@trouble.defaultvalue.org
[2]: id:87ios5v59p.fsf@nikula.org