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I'm currently writing a master thesis, which slowly became a real project which a "very big" institution is interested in using to create a product of their own. Eventually, I'll be involved in the implementation of this project (I'll be hired by them). My supervisor and my thesis partner (who is working remotely) still don't know about this.

I'm not sure how to proceed from here. Should I tell my supervisor and my thesis partner about this opportunity? Also, how can I write this thesis? Should I include them in the thesis? I need feedbacks and examples of similar thesis papers.

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    I don't see how you can not tell them. – aparente001 Apr 22 '17 at 0:54
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You'll need to carefully review your academic institution's intellectual property policies. Many academic institutions consider the work done by their researchers (including students) to belong to the institution, not to the person that created the work. If your institution has a tech transfer office, they would be able to advise you on how to legally patent and license your work for use by the "very big" institution. Also, your collaborators have a right to know how the work is being used (it belongs to them as much as it belongs to you), and you need their permission to share the work.

Note that I am writing this from an American perspective, so the legal (but not the ethical) portions of my answer may not apply if you are outside of the US.

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