Prevent negative interactions with module systems present in injected
pages and refactor browserify interactions with angular to increase
CommonJS accessibility / legibility and isolate angular module system
boilerplate.

- Avoid issues due to mis-detected module environments

  - In the injection script, load only Annotator and jQuery in the
    global scope and then both removed with `noConflict()`. Both are
    loaded with browserify-shim, which prevents jQuery from registering
    itself against require.js, if present (fix #2026).

  - Be explicit about registration of common cross-frame components
    (fix #2090).

    - Lift angular glue into app.coffee. Individual components are
      exported as CommonJS modules.

    - Lift Annotator glue into bootstrap.js (renamed hypothesis.js).

- Break up all modules that contained multiple services/directives/etc,
  such as the formHelpers and uiHelpers modules, as well as catch-all
  files like services.coffee and directives.coffee. For a summary of
  these movements see the bottom of this commit message.

- Rename all services, dropping the -service suffix, to match their
  injected names. This is consistent with how directives are being
  treated, and controllers as well (controllers are registered and
  injected done with the "Controller" suffix).

- Move Annotator subclasses into the annotator subdirectory. This
  change avoids having `Annotator.Host` clash with the `host`
  service and makes it easy to glob dependencies in assets.yaml to
  minimally rebuild either the app or the inject.

---

Summary of structural reorganisation. Modules that have been trivially
renamed (from "foo-service" to "foo") are not included in this list:

    controllers:AppController                   app-controller
    controllers:AnnotationUIController          annotation-ui-controller
    controllers:AnnotationViewerController      annotation-viewer-controller
    controllers:ViewerController                widget-controller

    directives:match                            directive/match
    directives:repeatAnim                       directive/repeat-anim
    directives:whenscrolled                     directive/whenscrolled

    directives/thread:pulse                     pulse

    filters:Converter                           filter/converter
    filters:momentFilter                        filter/moment
    filters:personaFilter                       filter/persona
    filters:urlEncodeFilter                     filter/urlencode

    guest                                       annotator/guest
    host                                        annotator/host

    helpers/form-helpers:createFormHelpers      form-respond
    helpers/form-helpers:formInput              directive/form-input
    helpers/form-helpers:formValidate           directive/form-validate
    helpers/string-helpers:createStringHelpers  unicode
    helpers/tag-helpers                         tags
    helpers/time-helpers                        time
    helpers/ui-helpers:tabbable                 directive/tabbable
    helpers/ui-helpers:tabReveal                directive/tab-reveal

    searchfilters:QueryParser                   query-parser
    searchfilters:SearchFilter                  search-filter
    searchfilters:StreamFilter                  stream-filter

    services:DraftProvider                      drafts
    services:ViewFilter                         view-filter
    services:renderFactory                      render

    session/session-service                     session

    streamsearch                                stream-controller

Add details on how to run dockerised dependencies

Move CSRF handling into a tween

Scroll to login form when clicking sign in link

This fixes an issue that if the login form is already shown but the
iframe is taller than the window and scrolled down so that the form is
out of view, then clicking on Sign in would do nothing. With this fix,
clicking Sign in scrolls the iframe up to the login form.

Realtime notifications for pages with the same link

Namespaced NSQ

Simplify code

Some more cleanup / simplification about the "Refresh UX" PR.

Removed some dead code

Add an atom feed for /stream

Refresh welcome page

AppController listens to 'beforeAnnotationCreated'

By doing that it catches newly created annotations and clear the current
selection/search result for the newly created card to be visible.

Fix #1979

Sync annotation state after anchoring

It was never called when the anchoring was finished.
This code adds the missing sync.
It is required for show diff to work.

Fix #2041

Separate the Host service

.. from AnnotionUISync.

Earlier, the show/hide frame functionality was implemented as a
background functionality of the AnnotationUISync service,
and it was not directly available for the sidebar code.

This commit separated that functionality into a new service,
and exposes it over a public API.

The test have been updated accordingly, too.

Do angular magic differently

This commit changes how we trigger the refreshing
of the markdown previews in the editor.

It has to do with how angular apply / digest cycles
interwene and crash in some cases.

The change was suggested by @RawKStar77 here:

https://github.com/hypothesis/h/pull/2038#discussion_r26867418

Explicitly disallow implicit relative imports

Add tooltips on adder buttons.

Change text of the toolbar button to "New Note."

Use Lato as font for welcome page to make it visually consistant with our
website.

Require PyJWT>=1.0.0,<2.0.0

Replace flash service with angular-toastr

Add IE autodetect for dom-text-mapper Annotator plugin

JWT Bearer Tokens

Fix #2051

Autocomplete feature for tags

Introduce tagsService which will handle the necessary filtering of tags
and saving them into the local storage in an appropriate format.