Organization of Joomla Files on Host Server

Hello again

Since my last thread I have installed Joomla via FTP upoad including template with vendors data to get me started. So far so good.

However, I have a question regarding file organization on server. Up to this point, I have uploaded all files to the root 'public_html' which i understand to be the location where files need to be to be seen by public on web. But do all files need to be there?

Do all Joomla files really need to be in this file for Joomla to function?
Would it make sense to have a file folder outside of 'public_html' where I could upload all files [like new extension zip files, etc] that I could then transfer to the public side when necessary? If this is a good strategy, where should I create this [or these] files?

As of this point, I have these uploaded files mixed in with the joomla files and this concerns me that I might get in trouble if I need to reinstall joomla again and could lose some of these files, or if they are on the public side, others might have access to them that I do not want.

Another question along security lines. Which folders would you recommend that i protect with a password? I see that there are options for adding password protection to files and as long as it wouldn't affect joomla function and if there is something worth protecting then I would like to do so.

Thanks again

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