Remove index.php and subdirectory in url string

Question

I moved my site to a new hoster. Everything works fine (Images path's js css templates, all fine).

I adjusted all path's with Reelocate. But all the Link in the Navigation throw back this error message:

Not Found
The requested URL /subdirectory/segment_1/entry was not found on this server.
Additionally, a 404 Not Found error was encountered while trying to use an ErrorDocument to handle the request.

It must have something to do with the subdirectory

In the webroot I have a .htaccess with this:

RewriteEngine on
RewriteCond %{HTTP_HOST} ^domain.com$ [OR]
RewriteCond %{HTTP_HOST} ^www.domain.com$
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^(.*)$ /subdirectory/$1 [PT,L,QSA]

and then in /subdirectory I have this .htaccess

# Removes index.php from ExpressionEngine URLs
    RewriteCond $1 !\.(gif|jpe?g|png)$ [NC]
    RewriteCond %{REQUEST_FILENAME} !-f
    RewriteCond %{REQUEST_FILENAME} !-d
    RewriteRule ^(.*)$ /index.php/$1 [L]

# Remove www.
    RewriteCond %{HTTP_HOST} ^www\.(.+)$ [NC]
    RewriteRule ^(.*)$ http://%1/$1 [L,R=301]

RewriteEngine off

Do I miss something?

Thank you

---

Edit:

The sollution of Alexa Lohmeyer worked. Here is how it looks if anybody is intrested:

One main error was that I had RewriteEngine off which somehow even disabled removing index.php.

So the root .htaccess looks like this:

RewriteEngine on

#Remove www
RewriteCond %{HTTP_HOST} ^www.domain.com$ [NC]
RewriteRule ^(.*)$ http://domain.com/$1 [R=301,L]

#Hosting directive for pointing url to subfolder
RewriteCond %{HTTP_HOST} ^domain.com$ [OR]
RewriteCond %{HTTP_HOST} ^www.domain.com$
RewriteRule ^(.*)$ /subdirectory/$1 [PT,L,QSA]

And then in the .htaccess of the subdirectory it looks like this:

# Removes index.php from ExpressionEngine URLs
RewriteCond $1 !\.(gif|jpe?g|png)$ [NC]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ /index.php?/$1 [L]

# Removes subdirectory from url string
RewriteRule ^subdirectory/index.php?(.*)$ /$1 [L]

Answer 1

RewriteRule ^subdirectory/index.php(.*)$ /$1 [L]

This should rewrite your original url:

http://domain.com/subdirectory/index.php/segment_1/entry

as:

http://domain.com/segment_1/entry

If that doesn't work, are you able to move your .htaccess into the root of your site directory? Or does it have to stay in your subdirectory?

Here is a handy htaccess test site: http://htaccess.madewithlove.be/

Answer 2

How to remove index.php in ExpressionEngine site from iPage hosting

https://emineysprince.com/technology-tips/post/how-to-remove-index-php-in-expressionengine-site-from-ipage-hosting