Fixed an issue where non-CLR assemblies (such as "Setup.exe" files) were not ignored. ...

... This was causing ILSpy exceptions, and aborting the entire solution compliation.  This happens even when patterns matching the outputs were added to the "Assemblies": { "Ignored:" [] } array in the .sln.jsilconfig file.

To test, create a solution that has a WiX Bootstrapper in it that build successfully at compile time and outputs a non-CLR .exe file (i.e. the WiX "Burn" Bootstrapper fulfills this requirement).  Run JSILc.exe against the solution.  It will throw an exception at the line containing "AssemblyDefinition.ReadAssembly(fn)" shown below.  To fix, I wrapped the call in a try/catch in a static method that will return null -- and further, I remove items where Assembly = null from the array using a .Where(...) condition before the IEnumerable is converted to an array.

[ I have an example solution on the web at: http://brainslugs83.azurewebsites.net/LD27-Downloads/ClickClickBoom-Source-2013-08-30.zip ]