Cloner Plugin not Cloning

Hello WPMU DEV's

We used your suggested Cloner plugin for our Multisite network. The first time we used it, it worked just fine cloning a site. But now it has an error on the cloning process.

Our Hosting Manager did some testing with it and found:

So the issue with the clones is a missing file in wp-content/themes/lms ... the entire "inc" folder is missing including the required file inc/template_tags.php

[10-Nov-2016 14:58:04 UTC] PHP Fatal error: require(): Failed opening required '/srv/www/www.tutoringclub.com/wp-content/themes/lms/inc/template-tags.php' (include_path='.:disappointed:usr/share/php') in /srv/www/www.tutoringclub.com/wp-content/themes/twentysixteen/functions.php on line 353

Curious how those files could have been misplaced, as I have never explored their contents?

Here is a successfully cloned site: https://www.tutoringclub.com/naperville/

Our site is hosted on a hidden IP (you may already know this), so for you to connect to it you need to adjust your hosting. Here is the Mac directions to access it:

1) Open Terminal in Applications>Utilities> Terminal
2) Type sudo nano /etc/hosts then hit return.
3) You'll be asked for your password. Enter your admin password.
4) move the cursor using the cursor keys and position it after the text you see, then type this:
54.70.175.116 http://www.tutoringclub.com
NOTICE: after 116 hit tab, then type http://www.tutoringclub.com
5) Then hit control + o
6) Then enter.
7) Now you can close terminal.
8) Navigate to http://www.tutoringclub.com and you should see the new site.

Let me know what you think, and thanks for your help,
Luke