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I have web app, call it Company, on one of it's site collections I have a site, call it IT.
I need to take IT site and make it as new site collection. I read here, SharePoint 2013 - restore a single site from site collection backup that it is impossible to restore just a site from site collection backup.

Export/Import is not an option due to export "flaw" not to save workflows from site.

I also tried with site template feature from OOB option in SP, but it doesn't support some of these features that I need to transit with site and it's content:
1. Customized permissions,
2. running workflow instances,
3. list item version history,
4. workflow tasks associated with running workflows,
5. publishing pages and publishing sites, etc.

Is there any way to take that IT site and make it as new site collection?

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Ootb this is not possible as every option have their own limitations. You already mentioned those.

Now only choice is use third party tools which help you to get this done. You can try sharegate as they not too much costly also offer free trial.

http://help.share-gate.com/article/914-promote-a-site-to-a-site-collection

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  • Thank you on your time, but we cannot use third party apps. – Danilo Jul 25 '16 at 14:18
  • That is limitation of this due to complex structure of site collection – Waqas Sarwar MVP♦ Jul 25 '16 at 14:20

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