Make the bridge service a factory instead

 - Remove unused support for options
 - Simplify the handling of scope
 - Make it a simpleton, and register the class as the constructor function.

Also updated all tests.

Kudos to @tilgovi for the feedback and ideas.

Fix sidebar's focusing on annotation cards

When the user moves the mouse over a highlight in the document,
the corresponding annotation card (in the sidebar) is supposed
to be highlighted, to indicate focus.

Our mechanism for this was broken in 3 different ways:

1. AnnotationUI service's focusAnnotations() method was working
   with annotation IDs. However, annotations being created
   right now don't yet have ID, only tags. So we should be working
   with tags instead. (Like we are, in many other cases
   when cross-frame communication communication is done
   around annotations.)

   I fixed that, and also updated the corresponding tests.

2. In controllers.coffee, when we were trying to check if a given
   annotation has focus, we were using the tag value, while on
   the other hand, it was not the tag, but the id that was put
   into the map. Of course this didn't work.

   Since now we are consistently using the tag, no change
   was needed here.

3. We are putting $$tag:true pairs into the map, but when
   checking for membership, the `in` operator was used.
   That works for lists, but not for maps. For maps, we simply
   have to read out the value belonging to the given key,
   and see if it's true.

After fixing these problems, the feature works again.

Replace type() typechecks with isinstance()

I will let it have its way.

That shaves ~50kB off the minified bundle.

Close #2019

Fix #2013

Use the jQuery from `Annotator.$`.

Remove dead things, move specific things, rename things.

- Drop the unmaintained Vagrantfile
- Drop the SSL cert
- Drop MANIFEST.in for setuptools_git (Close #1329)
- Move install docs into docs
- Move config files into config

Improve separation of h.api

Fix replies hover highlight

Clicking on the share icon didn't result in the share link being shown.
For now, the simplest way to fix this is to ensure that we get the
correct container element by using event.currentTarget (which will
always be the <a> tag) rather than event.target (which might be the <i>
tag).

Previously, the event from the initial click on the "share" event was
swallowed by the click handler on the parent thread:

    https://github.com/hypothesis/h/blob/fef9f43/h/static/scripts/directives/thread.coffee#L198-L221

Removing this has meant that the share dialog never shows.

Incidentally, this also fixes #1802, which was caused by the same code
in the thread directive, which swallowed all click events from its
children and hence prevented the closure of the share dialog.

The reply count being drawn in the thread directive causes display
issues if we want it to be in its current position alongside the
annotation controls.

This change moves the responsibility for (optionally) drawing a reply
count into the annotation directive. It results in simpler, clearer CSS
and in particular makes it possible to trigger a click event on the
reply count element.

It doesn't make any sense to uncollapse threads which have no replies,
so bake this into the toggleCollapsed method of the ThreadController.

Refine extension differentiators

Thread collapse clarity (and code clarity improvements)

This moves almost all of the logic determining what bits of the thread
to render when out from the template and into the controller where it
belongs.

Make threads start collapsed. This is possible because it now doesn't
affect the visibility of top-level cards.

The meaning of "collapsed" in the context of a thread was immensely
confusing:

- on a top-level annotation card it referred to whether replies were or
  were not shown
- on a reply, it referred to whether or not the entire annotation was
  hidden

This change removes all reference to the latter meaning. Annotations
(and replies) are still hidden appropriately when searches are
performed, but now collapsing and uncollapsing refers only to the
visibility of the *replies* of the addressed thread.

With the viewer template managing the root container, this is no longer
necessary.

This stops thread cards with no replies changing in height when clicked.

Also removes one unnecessary ng-hide directive.

Accoring to the thread directive options this component is optional. It
is, however, used extensively by the directive template. This isn't a
nice fix, but it does make it possible for the thread tests to pass.

The thread directive is doing rather a lot:

- rendering a list of cards
- rendering a card
- rendering a reply within a card

This change relieves the thread directive of the first of these
responsibilities.

The require'd 'thread' controller is not used.

Move frontend tests alongside tested modules

Use argparse to implement the main hypothesis CLI