block directory in .htaccess?

I have Joomla installed in the root & SEF Advance working. However, I added a non-Joomla folder at the root level, and now the file paths used by the program I'm running are messed up.

1. Is there a away to disallow mod rewrite on this non-Joomla directory? or,

2. If I install Joomla in a subdirectory, is it possible to remove the /joomla in the URL with this plug-in so that it appears my files are in the root directory, and thus a shorter URL?

TIA

I'm not an htaccess expert by any means, and I don't entirely understand your question. That said though, I have several sites that have other non-joomla folders in their root; including other php scripts. I don't have problems with the root htaccess nor SEF Advance interfering with sub directories. Perhaps you could place a clean htaccess in the folder your having trouble with.

The only thing I can think of that would cause problems is if you have a section / category name the same as the name of your folder. For instead you have a section called 'foo' and then you create a directory 'foo'. I would think that could definitely cause problems and one or the other would have to be renamed.

Hope that helps.