Rather than the thread-reply and thread-load-more elements having
one set of conditions on the parent and one on the child we now ensure
that the entire element is always shown/hidden.

Rename Heatmap -> BucketBar.

Ref #1236

Don't use target="_blank" for feedback email.

Consolidate code paths around deciding about PDF.js

Rename rpc methods to be more consistent

Annotator's PDF.js plugin replaces the document plugin
for PDF.js, so when we are using the PDF plugin, we
don't want to load the document plugin.

For this, we are removing it from the options, in
presence of PDF.

This commit changes how we test for PDF.

Earlier, we were simply testing for the presence of the
global PDF.js object, but it's better to actually
use the test already implemented inside the PDF plugin.

This has two benefits:
 * If the PDF plugin is not present, we won't
   mistakenly  remove the document plugin.
 * If the PDF plugin decides that it can't deploy,
   for whatever reason, we won't
   mistakenly remove the document plugin.

Between guests <-> sidebar
- `showViewer()` to  `showAnnotations()`
- `updateViewer()` to `updateAnnotations()`
- `toggleViewerSelection()` to `toggleAnnotationSelection()`

All these renames were to enforce encapsulation and these calls
are more like APIs. To guest side really do not have to know anything
what the sidebar has or does.

Renamed a few methods to be more consistent

(As previously discussed with @tilgovi)

Sidebar -> Document RPC methods:
 * Renamed `scrollTo()` to `scrollToAnnotation()` (to be consistent with `focusAnnotations()`

Guest methods:
 * Renamed `showViewer()` to `showAnnotations()` (to be consistend with `focusAnnotations()`)
 * Renamed `updateViewer()` to `updateAnnotations()` (same reason)
 * Renamed `toggleVIewerSelection()` to `toggleAnnotationSelection()` (same reason)

This reverts commit eb3c486991d921a1f2342a289cb9755d9d76459e.

I don't think this fixed anything because the permissions plugin
should still have been setting the permissions to empty.

It is fine if the permissions are initially undefined.
Fix #1747

Create reindex.py, add warning on mapping conflict

Update License and Notice files

Highlight state considation

Re-implement hiliting annotation cards on hover

Remove strings from the privacy template

Instead we use a method on the scope to determine the current
permission level.

Focus share link when pop-up opens

Sticky privacy on the browser

Use an object for privacy level models

Rename some things to be consistent about how we treat highlight
states.

- Use blue highlights for focus no matter whether active highlights
  are on or off.
- Use `setFocused` instead of `setActive` when setting the focus.
- Rather than `setViewerFocus` and `setFocusedHighlights` have
  symmetrical RPC calls named 'focusAnnotations` in both directions.
- Get rid of the multiple highlight levels for focus. When showing the
  focus it's not important to darken inner highlights. The highlights
  visible mode still has multiple levels, all yellow.
- Remove the "annotator-hl-temporary" styles since we never call
  `setTemporary` anymore.
- Remove the "finalizeHighlights" event because nothing listens for it.
- Rename the scope method `isFocused` to `hasFocus` because I have a
  general preference against participial adjectives. It is much easier
  to remember always to use the basic verb or noun meaning of focus,
  with no ending. `hasFocus`, `focusAnnotations`, etc.

Removing dead code from our annotator branch and dropping the '-ed'
suffix from class names is left out for simplicity of managing a single
PR against one repo for the moment, but may be advisable.

Provide a feedback button in the interface

This makes the association between the level key name and the display
text explicit and tight in the code.

Meant to resolve #1653. As per @dwhly's suggestion the dropdown menu is now accessible even when not logged in. Note: items relevant to only logged in users are not shown.

So that
 - Instead of a map, we now store a list of focused tags
 - The check for being focused has been moved
   into a method in the controller
 - The sidebar now exepts simply a list of tags to
   focus on (no more add/remove tags to existing list)

Don't bother looking up the annotations (for the tags),
since we only need the list of tags anyway.

(It was different when we worked with the IDs, but we
moved to use tags instead, so the actual annotations
are no longer needed.)

Restructure Chrome Extension

... because new and deleted annotations don't have IDs,
only tags, assigned by the bridge.