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We have a site where we need to be able to control both front-end and back-end permissions on a per-site level.

Our site structure is as follows:

Main Site / Main Domain: All can access is ok
State Site / Sub Domain: Restricted access - front-end via cookies, back-end via permissions

They, for SEO reasons, would like their URLs to look like this:

Main Site / Main Domain: www.mydomain.com
State Site / Sub - Domain: www.mydomain.com/state

Does it matter if we use sub-directories, or would we need to use actual sub-domains for this? Or is there any other reason to use a sub-domain vs a sub-directory with MSM?

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I've done both. The only thing you'll have to consider it making sure your cookie domains are set correctly, depending on if it's a site2.domain.com or domain.com/site2. Otherwise, the MSM sites will function exactly the same.

Past that, at most you have the regular head aches that could come from migrating a site, including getting .htaccess rules set correctly, and possibly dealing with hard coded links in templates in layouts and content, but that could also be fixed with .htaccess rules if you know what you're doing. Also, you'll have to make sure the introduction of /state to your main domains URI scheme isn't in conflict with any existing routes that start with state.

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Well, both things are fine in the terms of MSM. You can create sub-domain as well as sub-directory also. Just you need to take care is, about path settings at the time of setting MSM website.

And if you want to make SEO friendly then, yes sub-directory is the best option.

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