DW, Stop rewriting my code! pt 2 (bootstrap)

I'm not sure how long this has been going on, but today i discovered that when I open a file in DW that I have wrirtten OUTSIDE of DW, it rewrites it. It adds FOUR bootstrap lines to my <head>

<link rel="stylesheet" type="text/css" href="/bootstrap/css/bootstrap.css" />
<link rel="stylesheet" type="text/css" href="/bootstrap/css/bootstrap-responsive.css" />
<script type="text/javascript" src="/ScriptLibrary/jquery-latest.pack.js"></script>
<script type="text/javascript" src="/bootstrap/js/bootstrap.js"></script>

And towards the end of the file, it REMOVES a line: 

<script src="/assets/jquery/jquery.min.js"></script>

I have the NEVER REWRITE CODE option checked in preferences, and all the neccessary file extensions listed.  Yet it still rewrites my code, and has been for some time, destroying my work.

To the point where I cannot / will not even use DW anymore.  Which is a d@%# shame.

If I say DO NOT REWRITE MY CODE, then

DO. NOT. REWRITE. MY. CODE.  

Ideas? Suggestions?

Thanks.

ADDENDUM:  also notice related issue where when I open pages that have been created outside of DW for the first time, i get this popup (you have a spelling error too, btw... see attachment), which creates BOOTSTRAP and SCRIPTLIBRARY folders within my local site and proceeds to insert the above lines of code into my file.

Please stop trying to think for me!  I simply want to use DW edit my code. If you wont allow me to do so without rewriting it without my permission, I'll have to reccomend that we stop using DW.

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