Allow input path to be absolute.

I passed an absolute path to `compile-modules` and was surprised to have it generate the whole tree of directories into the output directory.

```bash
~/Projects/es6-transpile$ compile-modules ~/Projects/es6-transpile/foobar.js --to compiled
~/Projects/es6-transpile$ tree compiled/
compiled/
└── Users
    └── xtian
        └── Projects
            └── es6-transpile
                └── foobar.js

4 directories, 1 file
```

This change makes the output tree relative to the current working directory when the command is run.