Better handling of file permissions

[sandersky]

When using nodely on a Node project, it'd be nice to maintain the same file permissions on the output files that are found on the source files. For example when writing a Node script where src/index.js is actually going to be run via something like node ./lib/index.js, we'd typically do something like chmod +x ./lib/index.js to make it executable. However seeing as the lib directory isn't being checked into repos using this project, every dev that wants to do a build has to manually run the chmod command. Instead the chmod command should be done on the source file, which is checked into the repo. Nodely should then respect these file permissions when writing the output files, making it so devs never have to run chmod after the initial source file has been chmod'd and checked in.