rose suite-run/clean: configurable run root

The root location to place the directory of running suites can now be
configured via the `root-dir` configuration. `rose suite-run` now
generates a file for related configurations for `rose suite-clean`.
t/rose-suite-run: add remote run root test
rose suite-clean: now runs cylc refresh -u

And ensure that broken symlinks in `~/.cylc/` are removed.
rose suite-run: root-dir: update documentation
t/rose-suite-clean: more robust test
Merge pull request #1005 from matthewrmshin/rose-suite-run-root

rose suite-run: configurable root