When I “publish” or “package” the Azure “cloud service” WCF that I have, does the publish or package actually include the source codes for my application or is just the binary that is getting published. Is there a way that Microsoft can see the code of my application? Is it safe to assume that the actual C# codes are not being published or be seen in the Microsoft server? If binary is being published, there is no way for a binary to be reverted back to source code right? I’m just trying to protect my intellectual property.
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The binaries get deployed.
Any .NET library can be decompiled pretty trivially, though there are obfuscation tools that make the decompiled code more difficult to read (See Open Source Alternatives to Reflector? for a discussion on open source decompilers).
Personally I wouldn’t be concerned about Microsoft decompiling and stealing your IP. Anyway, any hosting provider would have similar access to your deployments.