Fix missing files

[code-asher]

Before:

After:

As near as I can gather it goes something like this:

1. Optimizer traverses imports and adds the code to the bundle
2. Optimizer excludes files in the resources array
3. When the optimizer excludes a file it also excludes all of that file's imports (and so on)
4. As a result if a bundle imports file A which is not in the resources array but is imported by another file B which is in the resources array it will 404 because file A is not bundled due to being excluded and not copied since it was not in the resources array.

We cannot put all files into the resources array to fix this either because as we previously discovered that results in the multiple top-level define error (when nothing is bundled the bundler appears to generate an invalid bundle; the output is completely different). And we want bundles anyway since they will provide a faster experience.