Scriptalias

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How do I enable CGI execution in directories other than the ScriptAlias?

Apache recognizes all files in a directory named as a ScriptAlias as being eligible for execution rather than processing as normal documents. This applies regardless of the file name, so scripts in a ScriptAlias directory don't need to be named "*.cgi" or "*.pl" or whatever. In other words, all files in a ScriptAlias directory are scripts, as far as Apache is concerned.
 
To persuade Apache to execute scripts in other locations, such as in directories where normal documents may also live, you must tell it how to recognize them - and also that it's okay to execute them.
 

In an appropriate section of your server configuration files, add a line such as
AddHandler cgi-script .cgi
The server will then recognize that all files in that location (and its logical descendants) that end in ".cgi" are script files, not documents.

Make sure that the directory location is covered by an Options declaration that includes the ExecCGI option.

 
In some situations, you might not want to actually allow all files named "*.cgi" to be executable. Perhaps all you want is to enable a particular file in a normal directory to be executable. This can be alternatively accomplished via mod_rewrite and the following steps:
 

Locally add to the corresponding .htaccess file a ruleset similar to this one:
RewriteEngine on RewriteBase /~foo/bar/ RewriteRule ^quux\.cgi$ - [T=application/x-httpd-cgi]

Make sure that the directory location is covered by an Options declaration that includes the ExecCGI and FollowSymLinks option.