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Aegir doesn't support having multiple sites in "subdirectories" (like example.com/foo and example.com/bar) yet that is a multisite feature that is supported in core and widely used in higher-ed institutions or organisations that do not have good control over DNS.
Having this feature would also make it easier to have multiple sites in a local dev environment as only one DNS record would be necessary.
There is a working solution in contrib: Mig5's Aegir Subfolders. The current plan is to incorporate this extension into core, as an 'experimental' feature.
From a front-end perspective, it simply adds a 'Subfolder path' field to the site form, which is both saved to the database, and passed to the backend to be saved in the site context (alias/entity). It also requires that we set an alias in the format "yourdomain.com.<subfolder>".
On the back-end, we create a stub.d directory in the /var/aegir/config area that is *not* pre-loaded/included in the server-wide context, but rather is included by our platform's Apache config at the right time. On platform verify, we inject a snippet that instructs the platform-level Apache config to include our special RewriteRules per server across this platform, *before* the .htaccess is included.
On site install (and verify and deploy), we stick an Alias one-liner for this site in a server-wide config. This can't go in the site's .stub file along with its Rewrite rules, because that .stub file gets Included within a directive, which can't contain Alias directives. We then symlink the subfolder name into the top-level of the Drupal root itself. We also insert our RewriteRule overrides per site into a .stub file which the platform-level Apache config includes.
When we disable a site, we inject a 'disabled site' rewrite rule into our stub so the site is disabled under its 'subfolder' URL. On site deletion, we delete the RewriteRule stub file along with the subfolder symlink in the platform root and the Apache mod_alias stub file.
This module has a number of documented issues we'll need to resolve along the way. These, along with the tasks required to merge it into core follow.
The tasks required for merging in 2.x would be:
Move subfolder.drush.inc into provision/subfolder
Move hosting_subfolders into hosting
Add a Hosting Feature for subfolders
Apply the included patch to clone.provision.inc.patch
5. Refactor provisionService_subfolder as an Aegir 2-style service.
Those tasks would be optional, in priority:
1. Perhaps add/improve validation of the 'subfolders' field (re. "2. Specify a 'subfolder'. No opening or trailing slashes")
2. Perhaps implement a full service that attaches to servers, which would get us automatic 'verify' tasks on all platforms.
3. Add support for renaming the subfolder when a site is renamed, or get to set a new subfolder for a site that is going to be cloned
4. Delete the old subfolder stub files when it's renamed, so have a concept of 'old' subfolder name vs 'new'.
5. Autocomplete the subfolder name based on the first part of the subdomain name
6. Autocomplete the 'example.com.prefix' Site Alias too.
7. Add Nginx support
User interface changes
(New or changed features/functionality in the user interface, modules added or removed, changes to URL paths, changes to user interface text.)
None so far.
Original report by redndahead
Talking with anarcat on irc it seems aegir doesn't support creation of mysite.com/site1 and mysite.com/site2 type of sites.