reorganize who knows what about paths

- add NotebookApp.notebook_dir
- add KernelManager.root_dir
- remove NotebookManager.notebook_dir, move to FileNBM.notebook_dir

Default value for KM.root_dir and fNBM.notebook_dir is NotebookApp.notebook_dir, but they can be configured separately.

SessionManager passes the API path to KernelManager,
which is responsible for turning it into the kernel's cwd.
use NotebookManager APIs in nbconvert handler