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If I create some custom pages that include custom html, css and jquery and this page exists within a site that is used as a site template, will that cause issues? From my limited experience with this whatever exists within a site is essentially a baseline, items within libraries (like jquery library) get created and copied??

Any and all advice and info is appreciated.

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Yes, if the assets are stored in a document library and you save the site as a template, the assets will be there when provisioning a new site off the template.

It may be a better approach though to bundle those assets into a feature and deploy them so they reside in the _layouts directory. If you need to make a change in the CSS or find a bug in the javascript, you can update the files in your feature and redeploy once instead of finding and replacing several files.

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@PirateEric...thanks for the information. appreciated. –  Justin Dec 20 '12 at 2:15

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