Fixed bugs that occured when transpiling files in other directories

[derekxu16]

• The paths for library files weren't being resolved properly when they started with ../ or ./ so TS names weren't being converted to Dart properly (ex. Array and List)
• Files weren't being transpiled if their paths began with ./ because SourceFile.fileName strips leading ./
• The generator was already writing files to subdirectories but was still generating imports as if all files were being output to the same directory

[jacob314]