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Improve Security on Free Software

I'm relatively new on Free Software, is very dificult to me using free software developing tools because I have learned developing with the Microsoft's tools from the beginning.

Then a teacher showed to us about the free software alternatives for developing and I was interested on them. One of my worries about the free software is this:

If I get for free all the source code of an application (like the database connection, encryptation algorythms, functionality) developed for my clients, everybody could know how this application works and maybe how to hack it!

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Microsoft is the Devil?

I read in network world where Microsoft's' Steve Ballmer has rekindled fears of Patent infringement in the Linux Kernel. I freaking hate Microsoft. My job depends on Microsoft staying alive but I hate'em just the same. I can appreciate that Bill Gates made MS what it is but give somebody a break with the IP stuff. They are not so far out of the last antitrust suit that they have to go looking for another fight are they? But if M$ keeps going Linus has to say something about this...where is he?

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