Minor User Guide update.
Minor pre-release User Guide update.
Adjust reference test suite timeout values.

I checked how long each suite took to run, and some of the timeouts were
a bit too tight - we probably need some leeway for slow or overloaded
suite hosts.
Removed obsolete CylcSim test program.

This was only relevant to pre multi-threaded cylc.
New HTML change log summary.
Moved CommsTest program to dev/
Merge pull request #260 from hjoliver/pre-5.0.0-changes

Pre 5.0.0 changes