Added support for including assets by relative path in bundle.txt

Sometimes you don't want to move files around into different directories to be able to create a bundle with them. For example, if you're pulling in jQuery via nuget, you probably want to leave the .js in ~/Scripts and create a jQuery bundle that references that .js and an external CDN url.

Before, adding files by directory (which was used for bundle.txt) only added files in that package directory, even if the bundle.txt included relative paths to other files (like ~/Scripts/jquery-1.11.0.js). I added an extra check on add to ensure that allFiles is properly populated with relative path references from Assets.

I also removed a couple of extra allocations done by unneeded .ToArray() calls.

This also fixes #244.