rose suite-run: configurable root

This change allows the real location of `~/cylc-run/$NAME` to be configurable via the setting `root-dir` in the Rose site and user configuration as well as in `rose-suite.conf`.

On a successful `rose suite-run`, it will create a file `~/cylc-run/$NAME/log/rose-suite-run.locs`, a Rose configuration containing the detail of the install locations. This file can subsequently be used by `rose suite-clean` to determine what to clean.

As part of this change, `rose suite-clean` has been enhanced to call `cylc refresh --unregister` as well as do a clean up of any broken symbolic links in `~/.cylc/`.

Provide the main enhancement for #945.