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In general, what penalty do you provide to an employee that takes company Intellectual Property away (violating the non-disclosure agreement)?

What is the best way to protect our bigger value (source code)?

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You have to decide whether it's worth going after him in court. In the US, you'd probably have good claims for breach of contract, misappropriation of trade secrets and copyright infringment. In Italy.... Well, see a lawyer.

As to 'how to protect' the code . . . Hire people you trust, do background checks if appropriate, and then use internal controls to segment the code that individuals are allowed to look at.

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Regarding U.S. can you ask employees to sign a contract that includes a heavy fee for it? – devdept Apr 26 '12 at 6:41
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Not easily. In the U.S., "Penalty Charges" for breaches of a contract cannot be enforced. But, if the fee approximates the damages that you would incur as a result of the breach, then it would probably be legal -- that's something called 'liquidated damages.' – Chris Fulmer Apr 26 '12 at 12:05
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If you can't come to agreement with the person who took your IP the only recourse may be for both of you to make some lawyers a little richer. The best thing to do is not to hire people you can't trust.

Having said that I have stored some very proprietary source code in a library that was stored in version control with the rest of the source, but only highly trusted employees (3 in addition to myself) had access to that module. The binary for the library is distributed with the application and is available to anyone in the company, but access to the source is very closely guarded.

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Honestly after 12 years of wedding I'm not sure I can trust my bride, yet. How can you bet on one employee? – devdept Apr 26 '12 at 6:39
The employees I've worked with for a decade and are invested in the company get a higher level of trust than the guy I hired off the street last week. If you can't trust anyone with your trade secrets it's going to very hard to scale your business. The 2nd paragraph of my answer discusses how I handle it. – Jim Blizard Apr 27 '12 at 14:28

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