The .htaccess file and converting site to https

Actually I need to do this as well (convert site to https).  Using Modx Revo 2.5.7-pl.  Ive broken
my site my editing my .htaccess files in trying to implement cute url's but generally got it back.
However, now Modx gives me a warning that my core directory is available for anyone to view: which
I presume is undesireable.

If I disable the .htaccess file, then I cannot load the Modx manager.  It should permit control 
by the Apache Server and is thus unecessary. However if I enable it, it seems to give everyone
access to my core directory.  The contents of the .htaccess are as below.  Note I've change my
domain to my-domain.      Finally I was preferring to use [u]my-domain.com[/u]  NOT www.my-domain.com
 You'll note there are differences between the .htaccess file referenced elsewhere in some of the coding  

for example he has:
code]#RewriteCond %{HTTP_HOST} !^clientdomain\.com [NC]

RewriteCond %{HTTP_HOST} ^(www.)?my-domain.com$

# .htaccess main domain to subfolder redirect
# Copy and paste the following code into the .htaccess file
# in the public_html folder of your hosting account
# make the changes to the file according to the instructions.
 
# Do not change this line.
RewriteEngine on
 
# Change yourdomain.com to be your main domain.
RewriteCond %{HTTP_HOST} ^(www.)?my-domain.com$
 
# Change 'subfolder' to be the folder you will use for your main domain.
RewriteCond %{REQUEST_URI} !^/modx/
 
# Don't change this line.
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
 
# Change 'subfolder' to be the folder you will use for your main domain.
RewriteRule ^(.*)$ /modx/$1
 
# Change yourdomain.com to be your main domain again.
# Change 'subfolder' to be the folder you will use for your main domain
# followed by / then the main file for your site, index.php, index.html, etc.
 
RewriteCond %{HTTP_HOST} ^(www.)?my-domain.com$
RewriteRule ^(/)?$ modx/index.php [L]

ErrorDocument 404 "<H1>Page 404 not finding</H1>"

# Prevent Apache from serving .htaccess files:
<FilesMatch "^\.htaccess">
    Order allow,deny
    Deny from all
</FilesMatch>

Options All -Indexes
Options +FollowSymlinks

RewriteEngine On
RewriteBase /

RewriteCond %{HTTP_HOST} domain\.com [NC]
RewriteCond %{SERVER_PORT} 80
RewriteRule ^(.*)$ https://domain.com/$1 [R,L]

# The Friendly URLs part
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} !^/[0-9]+\..+\.cpaneldcv$
RewriteCond %{REQUEST_URI} !^/[A-F0-9]{32}\.txt(?:\ Comodo\ DCV)?$
RewriteCond %{REQUEST_URI} !^/\.well-known/acme-challenge/[0-9a-zA-Z_-]+$
RewriteRule ^(.*)$ index.php?q=$1 [L,QSA,NC]