Calling Captivate HTML5 Output from an application

I want to call Adobe HTML5 and Flash Captivate published output from an application.  There are several issues I'm currently experiencing duing this:
1) Iframe. 
Using an Iframe works for the most part, except that we are hosting many Captivate presentations and there's a bloated number of files when showing the presentation this way, since each one gets the full set of support files needed. 
There's also a bug when hiding and reshowing the Captivate presentation (using jQuery.hide and jQuery.show respectively on the parent form): when reshowing the video player controls disappear. 
To get around this I progammatically set the height of the iframe to zero, and then set it back to desired screen height when showing the presentation.
2) view in app.
I'm guessing this could work but there's such a mishmash of published files and resources, in our case over 200 in all.
There are several issues we run into in general:
1) jQuery in the published captivate is an old version of jQuery  2.0.0 is current.
2. jQuery ui in  the published captivate is an old version of jQuery.  1.10.2 is current.
3. [presentation_name].htm files do not capture javaScript events or open urls currently in the proesentation, only the index.html file does.
-David

The following Thread helped me to solve this issue...
Switching applications without logging in again
Thanks

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