Add a 'cwd' option, and misc refactoring and tweaks before simple config merging

[loganfsmyth]

Q	A
Fixed Issues?	Fixes #1, Fixes #2
Patch: Bug Fix?	N
Major: Breaking Change?	N
Minor: New Feature?	Y (added cwd option)
Tests Added + Pass?	Yes
Documentation PR
Any Dependency Changes?
License	MIT

Only new feature is adding a cwd option that Babel will used to resolve relative paths passed programmatically. Defaults to the global cwd. This I think is the last place where we were relying on global state, so technically we would have used the wrong filename in the transform if someone did

var opts = babel.loadOptions({ filename: "./file.js"});
process.chdir("/other");
babel.transform("", opts);

so now we allow an option for it, and loadOptions includes the value that was used in the opts it returns.

Everything else in here should be entirely non-controversial too.

[babel-bot]

Build successful! You can test your changes in the REPL here: https://babeljs.io/repl/build/5992/