I recently migrated my wordpress multisite from localhost to aws bitnami multisite. I used duplicator pro, deleted everything inside the wordpress/htdocs folder and ran the installer.php hrom there. Good news: installation was successful (Despite me thinking this way was stupid). Bad News : All the paths are messed up. The 2 main problems here are thus

1) All the css and js file links in the head tag are showing the path as mainsite/subsite/folderpath/filename.js instead of mainsite/folderpath/filename.js like in my localhost.

2) When I try going into wp-admin of any of the subsite using mainsite/subsite/wp-admin.php, it enters an infinite loop of redirects.

Now I gathered from different answers on stack that the issue is with the htaccess file/files in the conf folder. Frankly I can't understand what is in there so I simply tried copying the contents of my .htaccess file(standard multisite htaccess) into the different .conf files one by one to no effect. I am also not sure if position at which i pasted is the correct one.

I also added the following to wp-config as some answers suggested but didn't help:

define('WP_SITEURL','myip.xip.io');
define('WP_HOME','myip.xip.io');

Any ideas what i can do to fix this? Here are the htaccess.conf file after I added the multisite code:

# This file was updated by Duplicator Pro on 2019-04-21 09:03:51.
# See htaccess.orig for the .htaccess original file.
# BEGIN WordPress (3.5+ Multisite Subdirectory)
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]

# add a trailing slash to /wp-admin
RewriteRule ^([_0-9a-zA-Z-]+/)?wp-admin$ $1wp-admin/ [R=301,L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(wp-(content|admin|includes).*) $2 [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(.*\.php)$ $2 [L]
RewriteRule . index.php [L]
# END WordPress


<Directory "/opt/bitnami/apps/wordpress/htdocs/wp-content/plugins/akismet">
# Only allow direct access to specific Web-available files.

# Apache 2.2
<IfModule !mod_authz_core.c>
    Order Deny,Allow
    Deny from all
</IfModule>

# Apache 2.4
<IfModule mod_authz_core.c>
    Require all denied
</IfModule>

# Akismet CSS and JS
<FilesMatch "^(form\.js|akismet\.js|akismet\.css)$">
    <IfModule !mod_authz_core.c>
        Allow from all
    </IfModule>

    <IfModule mod_authz_core.c>
        Require all granted
    </IfModule>
</FilesMatch>

# Akismet images
<FilesMatch "^logo-full-2x\.png$">
    <IfModule !mod_authz_core.c>
        Allow from all
    </IfModule>

    <IfModule mod_authz_core.c>
        Require all granted
    </IfModule>
</FilesMatch>
</Directory>

Here is the httpd-prefix.conf which I haven't edited.

DocumentRoot "/opt/bitnami/apps/wordpress/htdocs"
#Alias /wordpress/ "/opt/bitnami/apps/wordpress/htdocs/"
#Alias /wordpress "/opt/bitnami/apps/wordpress/htdocs"

RewriteEngine On
RewriteCond "%{HTTP_HOST}" ^ec2-([0-9]{1,3})-([0-9]{1,3})-([0-9]{1,3})-([0-9]{1,3})\..*\.amazonaws(:[0-9]*)?$
RewriteRule "^/?(.*)" "%{REQUEST_SCHEME}://%1.%2.%3.%4%5/$1" [L,R=302,NE]

#Init xip redirection
RewriteEngine On
RewriteCond "%{HTTP_HOST}" ^([0-9]{1,3})\.([0-9]{1,3})\.([0-9]{1,3})\.([0-9]{1,3})(:[0-9]*)?$
RewriteRule "^/?(.*)" "%{REQUEST_SCHEME}://%1.%2.%3.%4.xip.io%5/$1" [L,R=302,NE]
#End xip redirection

Include "/opt/bitnami/apps/wordpress/conf/httpd-app.conf"