home url is putting index.php on end of address

Hey, so I have now got SSL on my site! my users can now use https. Yippee!

However, since then the home URL seems to be messed up.

for some reason
https://dustyghost.com
is becoming
https://dustyghost.comindex.php/

something of note here, my WordPress site is installed in a subdirectory.
So the home url of dustyghost.com loads a WP site located in a publicHTMl/dustyghost subfolder.

So I have 2 htaccess files:

in the website root dir:

# Use PHP70CGI as default
AddHandler fcgid70-script .php
# Changed PHP handler from application/x-httpd-php54s to application/x-httpd-phpbetas on Fri Dec 18 05:06:37 MST 2015.
Options -Indexes

Redirect 301 /tablet_tut.html https://dustyghost.com/marks-stuff/tutorials/graphics-tablet-making-the-change/

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine on
RewriteCond %{HTTP_HOST} ^(www.)?dustyghost.com$
RewriteCond %{REQUEST_URI} !^/dustyghost/
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ /dustyghost/$1
RewriteCond %{HTTP_HOST} ^(www.)?dustyghost.com$
RewriteRule ^(/)?$ dustyghost/index.php [L] 
</IfModule>

# END WordPress

RewriteEngine On
RewriteCond %{SERVER_PORT} !^443$
RewriteRule ^(.*)$ https://%{SERVER_NAME}%{REQUEST_URI} [R=301,L]

and in the dustyghost sub dir:

# Use PHP70CGI as default
AddHandler fcgid70-script .php
# Changed PHP handler from application/x-httpd-php54s to application/x-httpd-phpbetas on Fri Dec 18 05:06:37 MST 2015.
Options -Indexes

Redirect 301 /tablet_tut.html https://dustyghost.com/marks-stuff/tutorials/graphics-tablet-making-the-change/

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

# END WordPress

# Wordfence WAF
<Files ".user.ini">
<IfModule mod_authz_core.c>
	Require all denied
</IfModule>
<IfModule !mod_authz_core.c>
	Order deny,allow
	Deny from all
</IfModule>
</Files>

# END Wordfence WAF

RewriteEngine On
RewriteCond %{SERVER_PORT} !^443$
RewriteRule ^(.*)$ https://%{SERVER_NAME}%{REQUEST_URI} [R=301,L]

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