Copy the PDBs for the CLR host assemblies to the Engine binaries dir

For some reason VS2013 couldn't always find the PDBs on my machine while
debugging. Copying them to the same location as the assemblies means it
should have no more problems finding them.
Fix NullReferenceException being thrown in InitializeEngineAppDomain()
DestroyEngineAppDomain() must be invoked on default app domain manager
Update .gitignore
Fix wrong path in CreateLinks.bat