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Consider removing NInject dependency
The NInject dependency seems to duplicate functionality which is normally handled using MEF in the Visual Studio extensibility world. Introducing a different composition mechanism makes it more challenging for users to contribute to the code since the patterns deviate from the more well-known practices.
Personally I am not a huge fan of MEF, but I am open to the idea if it provides all of the functionality that we get with Ninject. Personally, I find Ninject very easy to work with and think that most developers can come up to speed on it in about 15 minutes so don't think it is a huge barrier to entry.
If MEF is used extensively in Visual Studio however, then Ninject might be redundant.