rose suite-scan: scan port files as well

Report left behind port files.
Report exceptions for failed `cylc scan` and `ssh` commands.
Merge pull request #1180 from matthewrmshin/rose-suite-scan-port-file

rose suite-scan: scan port files as well
Update for release 2014-03
rose edit: fix change meta or project flag.

This fixes changing the =meta or =project variable
within a rose edit session. Due to the old code's
reliance on ConfigNode data, which is not updated as
often, the update of the metadata does not get
triggered. This change adds the ability to source
the meta or project flag from the variable itself,
which is more correct.
rose config-dump: fix tidying metadata
rose macro, rose app-upgrade: fix relative opts.conf_dir
rose macro, rose app-upgrade: fix relative opts.output_dir
rose app-upgrade, rose macro: fix test-battery
rose app-upgrade: fix test-battery
Merge pull request #1184 from benfitzpatrick/rose-edit.fix-change-meta-flag

rose edit: fix change meta or project flag.
Merge pull request #1186 from benfitzpatrick/rose-macro.fix-conf-dir-relative

rose app-upgrade, rose macro: fix relative opts.conf_dir
Merge pull request #1187 from benfitzpatrick/rose-config-dump.no-pretty-namelist-metadata

rose config-dump: fix tidying metadata