Need help rebuilding lost htaccess file

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It’s tricky to do this…

Requests for any other subfolder (assuming it exists) should go through to to the folder requested (e.g. mydomain.com/proxy or mydomain.com/shop are passed through to their respective folders /proxy and /shop).

…in combination with…

Requests for subfolders which do not exist, should be routed through to mydomain.com/site

…without losing the ability to pass rewrites onto said subfolders. You see, something like…

RewriteCond %{REQUEST_URI} ^/site
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d  
RewriteRule (.*) http://www.domain.com/site/$1 [R=301,L]

…will hijack any URL that does not resolve to an actual resource, even if the initial path component points to a valid subfolder. For example, /proxy/no-file-here or /shop/product/dynamic-url will all get redirected to /site/...

Since I assume that’s not ideal (particularly for Magento), I suggest a blacklist of directories to ignore, then handle the rest of your demands.

<IfModule mod_rewrite.c>
  RewriteEngine on

  # Enforce www, use lexical comparison for efficiency.
  RewriteCond %{HTTP_HOST} != "www.domain.com"
  RewriteRule (.*) http://www.domain.com/$1 [R=301,L]

  # Stop rewriting for blacklisted directories 
  RewriteRule ^(proxy|shop) - [L]

  # Handle root domain & non-"/site" requests
  RewriteCond %{REQUEST_URI} = "https://wordpress.stackexchange.com/" [OR]
  RewriteCond %{REQUEST_URI} !^/site
  RewriteCond %{REQUEST_FILENAME} !-f
  RewriteCond %{REQUEST_FILENAME} !-d  
  RewriteRule (.*) http://www.domain.com/site/$1 [R=301,L]
</IfModule>

# Legacy Joomla rules here

# BEGIN WordPress
<IfModule mod_rewrite.c>
  RewriteEngine On
  RewriteBase /site/
  RewriteRule ^index\.php$ - [L]
  RewriteCond %{REQUEST_FILENAME} !-f
  RewriteCond %{REQUEST_FILENAME} !-d
  RewriteRule . /site/index.php [L]
</IfModule>

# END WordPress

I’m no Apache wiz, and although you’ve tried SO before, they still might be your best bet, if not even webmasters.