The rules that point to "-" are ignored by AWS:MRT because Abyss does not use these so-called dummy rules. They just instruct Apache to ignore the rule from what I understand. I am looking more into this problem.
UPDATE: 5/2/2014 @ 12:47 EST It turns out you might be able to use this with Abyss. The rules just remove index.php from the end of the URL, creating the illusion of full friendly URLs. With Abyss as well as other servers, queries to scripts can look like site.com/index.php/apps/files. All these rules do is remove the index.php if the resource does not already exist.
Try running these through AWS:MRT and see if it works. I do not have the script to test so this is just a guess.
RewriteCond %{REQUEST_FILENAME} !-s
RewriteRule ^.*$ index.php [NC,L]
UPDATE: 5/2/2014 @ 12:34 EST This forum topic explains it. Unfortunately, I don't think this will work with Abyss Web Server. Perhaps Aprelium can shed some light on things?
http://xenforo.com/community/threads/the-default-htaccess-file.47906/