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This is my current .htaccess.  I have a subfolder that contains another application not run by CI. What do I add to this .htaccess so CI will not treat this folder as part of the CI application framework.

RewriteEngine on
RewriteBase /

#Removes access to CodeIgniter system folder by users.
#Additionally this will allow you to create a System.php controller,
#previously this would not have been possible.
#'system' can be replaced if you have renamed your system folder.
RewriteCond %{REQUEST_URI} ^system.*
RewriteRule ^(.*)$ /index.php?/$1 [L]

#Checks to see if the user is attempting to access a valid file,
#such as an image or css document, if this isn't true it sends the
#request to index.php
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d

RewriteCond $1 !^(index\.php|images|robots\.txt)
RewriteRule ^(.*)$ /index.php/$1 [L]

Currently with this .htaccess any subfolder request at the end of the url goes to CI of course.

You already have a spot in there for that:
RewriteCond $1 !^(index\.php|images|robots\.txt)

Just add the folders you’d like to skip from being passed into index.php
RewriteCond $1 !^(index\.php|images|subfolder1|subfolder2|robots\.txt)

In my subfolder I have a .htaccess file for password authentication.  This is what appears to be causing the problem.  If I remove the .htaccess file from my subfolder it loads fine.

Any ideas how I can overcome this? subfolder needs to be password protected.

You must have another issue, because

RewriteCond %{REQUEST_FILENAME} !-f

should already be sufficient to stop the rewrite of a request for a valid file in that subfolder.

Finally found the solution in the forums.

RewriteCond $1 !^(401.shtml)

as I saw in another post needs to be added to root .htaccess before the last rewrite line.