File copy uses working directory

Currently, the file copy function uses the OS working directory.
This causes problems for multi-module projects.
If you run maven from the docker-containing project, it will have the project as the root directory.
If you run maven from the parent project, the parent will be the root.

The attached code explicitly sets the root directory as the root of the project that contains the docker plugin currently being processed.
If you don't care about backwards compatibility, this could be simplified to use the source directory for everything.