I didn't say it was fixed. What I said was that the js stuff in the /includes directory is for the *admin* area. if you edited the js stuff that's inside the includes directory so the jQuery for your *theme* would work, you've just messed up your admin area (which, as per your question, you did.)
if there was an error in the jQuery for your *theme* them there was an error in that jQuery code that needed to be fixed. You shouldn't have gone into the jQuery for the *admin* area (which is located in the /includes folder) and tried to mess with that. What you should have done is tried to fix the *theme* related jQuery code that belongs in your theme folder.
i.e. you fixed the wrong code, and messed it all up.
at least that's what I'm getting from your question - that the jQuery you were using for your theme wouldn't do what it needed to do. You say it kept "defaulting to the includes directory" - that sounds to me like you either put the code in the wrong place, or you didn't use the right call in your header to find the file. So yes, it is here or there.
What you need to do now is reupload the files you messed with in the includes folder, and revert them back to what they were. Then figure out why the jQuery you put into your theme header was getting the error it was getting - rather than trying to rewrite WordPress.
When you're working with the theme files, you stay in the wp-content/themes folder. You don't go poking around in core code...you're just asking to bang your head on a brick wall.