Took some unnecessary verbosity out of 'cylc help'.

The descriptions of pyro communication, suite passphrases, and ssh
messaging, belong in the User Guide, not top level command help.
This commit also tidies the corresponding sections of the user guide.
Removed a remnant of original batched job submission implementation.
This adds table of contents links to the single-page User Guide.

And mini table of contents at the top of each chapter, for the single
and multi-page documents.
Use html (not xhtml) with htlatex, both documents.

(makes no difference really)
Fix connection lost tracebacks from gcylc on suite shutdown.

This started happening relatively recently ( possibly after
multi-threading cylc?) although looking at the code I'm not sure why it
didn't happen earlier too. Anyhow, this commit also rearranges the guts
of the reconnect() methods to make them consistent between the three views.
Merge pull request #242 from hjoliver/command-help-tidy

Took some unnecessary verbosity out of 'cylc help'.
Merge pull request #246 from hjoliver/fix-gcylc-tracebacks

Fix connection lost tracebacks from gcylc on suite shutdown.
Merge pull request #243 from hjoliver/html-doc-contents

This adds table of contents links to the single-page User Guide.
Merge branch 'master' into final-config-changes

Conflicts:
	bin/cylc