Remove obsolete timeout documentation in gcylc help.

This also fixes a bug: suite run commands generated by gcylc were wrong
if the --pyro-timeout option was used.
Removed obsolete --from-gui command option, and associated code.
Corrected a typo in get-global-config command help.
Corrected typos in broadcast command help.
Make lockserver Pyro timeout option consistent with other commands.
Removed obsolete suite reload shell script.
Use Jinja2 --set options only where needed.
Hot fix for site/user config $HOME replacement in directory paths.

Only affects tasks running under other user accounts on suite host.
Comments in port file module.
Get rid of obsolete suite directories created under .cylc
Complete suite host housekeeping for test battery.
Added new test suite bin scripts.
Merge pull request #401 from hjoliver/test-battery-housekeeping

Test battery housekeeping
Merge branch 'master' into 387.command-help-errors

Conflicts:
	lib/cylc/scheduler.py
Merge branch 'master' into 387.command-help-errors
Merge pull request #400 from hjoliver/387.command-help-errors

387.command help errors