Comment out most options in the generated config. (#4863)

Make it so that most options in the config are optional, and commented out in
the generated config.

The reasons this is a good thing are as follows:

* If we decide that we should change the default for an option, we can do so,
  and only those admins that have deliberately chosen to override that option
  will be stuck on the old setting.

* It moves us towards a point where we can get rid of the super-surprising
  feature of synapse where the default settings for the config come from the
  generated yaml.

* It makes setting up a test config for unit testing an order of magnitude
  easier (see forthcoming PR).

* It makes the generated config more consistent, and hopefully easier for users
  to understand.