The htaccess rules provided in the plugin are not the only way to handle things. It is possible to "review" the requests coming in and compare them to the files and folders on the system. If they don't point to a valid file nor folder then they should be handled by the plugin.
This way as long as you don't have a file (with path) that exists in the store directory that is the same name as one of your products then it would work to have Zen Cart in the root directory and these other things still in the store directory at least for the time being.
Basically could have the htaccess, instead of excepting specific folders with the various RewriteCond's, to be like this:
Code:
RewriteEngine on
RewriteCond %{REQUEST_URI} ^/store(/)?$ [NC]
RewriteRule ^(.*)$ index.php [QSA,L,R=301]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php [QSA,L,R=301]
This way, if the requested path is not specifically an existing file or folder then it will be handled by your catalog. The first rewrite checks to see if the request is specifically for the root of the store without/with the ending slash. The second set processes the request, evaluates the file/folder structure to see if the specific request is a file or a specific folder. If it is either of those two, then no handling is performed. If path provided doesn't resolve to a file or folder then the request is provided to the code to process.
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