allowJs should default to true

[sandersn]

allowJs should default to true. It works well enough that there aren't significant downsides to using it.

It does, however, change some settings, such as JS resolution in node_modules, I think. I need to list those here before going ahead with this proposal.

[DanielRosenwasser]

The reason we didn't do this was because if you don't specify an outDir, you'll have an issue with your outputs overriding your inputs, or you'll have issues like recompiling your outputs over and over.