FileNotFoundException when building js-deps index, when emacs temp-file links are present in filesystem

When an emacs temp file link is in the filesystem next to its original js file the compiler fails to start with a FileNotFoundException.

This happens when a :libs path is provided and the directory is indexed.

Suggested fix: check for file existence when indexing the files with `js-deps/build-index`

and or don't include hidden files when indexing the directory.