i am wondering is kali linux 2.0 fully open source? What i mean by that what software and parts of kali linux 2.0 is closed-source? In kali linux official documentation (http://docs.kali.org/policy/kali-linux-open-source-policy) it says "Kali Linux’s non-free section contains several tools which are not open source." What are those tools and are they still here in kali linux 2.0?
Kali, like Debian, is fully open source. However, there are many closed source tools which might be of great interest to the Kali user and, as such, they have been made available through the
non-free repo. If you don't want any closed source software on your Kali distro, disable that repo.
If you are just a Kali user, then having closed source software on your machine shouldn't be a problem. The issues arise if you want to build a Kali derivative and distribute it; in this case, you must be fully aware of the restrictions in redistributing each piece of closed source software.
Short answer: Kali Linux is fully "Open Source".
Long answer: Since Kali contains "non-free" repos it is likely not considered "Free Software".
Non-free repos: http://http.kali.org/dists/kali-current/non-free/binary-amd64/
The FSF doesn't consider a given distribution "Free Software" if it provides non-free software, even in repositories. Kali does fit the Open Source Initiative's definition of "Open Source" however: http://opensource.org/, at least that is my reading.
By looking at the date of the "Packages" file in the above URL I assume that yes, those packages are in the latest version of Kali. If you want to know what those tools are you can read the Packages list directly since it provides a description of the files. You're likely to find firmware and data packages that are not released under an approved OSI or FSF license.