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I wrote a way to redirect to a main url of choice, rather than the main site url. In the process of writing this functionality, I realized that I may not actually need this functionality, I found that aegir has "automatic" aliases, and that I just have to change my process to get Aegir to do what I want it to do.
I'm posting this code here in case anyone finds it useful, or thinks this might also be a good idea to have this functionality. Essentially it just gives you another field next to the aliases to type in the url that you want your site redirecting to, and defaults to the main site url.
Note from the Aegir maintainers:
This issue overlaps with: