Q:

Pages in subdirectory redirect only to that subdirectory

I have my site in two directories, default is on root and the other is root/en. Is there a way to tell in .htaccess that every link we click on root/en version redirects to root/en?
For example I have a link on my default installation that leads to root/news. Now if the user is located on root/en and clicks this link it redirects him to root/en/news.
We always have /en prefix before our original links. Or do I have to go and change all the links manually?

A:

Rewrite won't work or will be extemely complex because you have the same files in both directories.  So Apache won't know how to tell which link you clicked unless you change all the links.  The quick way to change the base URL for all the links in your pages is to use the <base> tag.  Note that it will change the base URL for all relative resources such as css, javascript and images too.
If the links in your pages are relative (i.e. they don't have the http://www.example.com part), then you can use the <base> tag to set the base URL for all resources on the page.  See:  http://www.w3schools.com/tags/tag_base.asp
All of your pages in the /en/ directory should have a <base> tag that sets the base URL, and your links should start with /.
Example:

<html>
  <head>
    <base href="http://example.com/en/">
  </head>
  <body>
    <a href="/news.php">news</a>
  </body>
</html>

Here's an example of an apache redirect to a subdirectory, but I don't think it works in yoru case.  Browsers will not be able to access anything in the / directory this way:
RewriteEngine on
RewriteRule ^$ en [L]    

