Fix recursive include

There are two fixes:

1. Fix extern classes dependencies.
Extern classes was removed from fileDef in commit 1793cb884b465e40aed15e55049ef6b0bad40816
but it breaks dependencies resolving (no searching in extern classes)

2. Fix -R option.
if we use command with -R option "coffeescript-concat -R ./src/" sourceFiles is empty array and in function concatFiles we get sourceFileDefs also empty (because of filtering based on sourceFiles). Now if sourceFiles is empty we will get all files in directory.