Previously, an annotation with a selectorless target (such as a comment
or "page note") would be marked as an orphan.

This commit adjusts the orphan detection code so that an annotation is
marked as an orphan only if both of the following conditions are met:

- it has at least one target with selectors (an "anchorable target")
- none of the anchorable targets have successfully anchored

In order for comments (AKA "page notes") to be discoverable with the
search logic implemented in #2413 (cc4ca35), they need to have at least
one target with a source field.

Previously a comment was defined as an annotation

- with a `uri`
- without any targets
- without any references (no targets but with references == a reply)

Now comments have a single target with a single field, `source`. This
finally puts us in a position where we can consider deprecating the
`uri` field.

If one of these asserts fails, then this test will timeout (taking 2
seconds to do so).

By using a small helper (`timeoutPromise`) to implement the "next tick"
functionality that was previously achieved with `setTimeout`, this is
improved: we return a promise from the test function and a failure will
be reported immediately.

See https://mochajs.org/#working-with-promises for more on returning
promises from mocha test functions.

It's not at all clear from the code that the singular "selector" is in
fact an array of selectors referring to a single target. Add a few
comments to help understanding this until we can sort out a better
refactoring/naming.

The last thing that used this was removed in 7829cc1.

Change $anchored -> $orphan

Instead of setting $anchored=true on anchored annotations, set
$orphan=true on orphaned (i.e. unanchored) ones as we used to do.

Orphaned annotations are the exception: we don't show them, or if
show_unanchored_annotations is one then we show them with a warning.
It's simpler and less buggy to add $orphan=true onto the exceptional
annotations than to try to add $anchored=true onto all of the
unexceptional ones.

Fixes #2525.
Fixes #2541.

Fix document title and domain for local file PDF annotations

This fixes two issues on the annotation cards for some annotations:

1. If the annotated document has a non-http(s) URI (e.g. a local file://
   URI) then don't hyperlink the document's title to that URI

2. If the annotated document has no .domain value or its domain is the
   same as its title then don't display anything, instead of displaying
   a pair of emtpy braces ().

To fix this move the logic for formatting an annotation's document's title
and domain into AngularJS filters where it can be tested, instead of in
the template.

Use autoprefixer to add vendor prefixes to CSS

Translate annotation mapper

Hide unanchored warnings when not sidebar

Don't show the "We can't find the exact position of this annotation"
warnings on unanchored annotations when on the stream or individual
annotation pages - only show them in the sidebar.

Fix an issue where the group details container
could horizontally overflow the dropdown menu.

In IE 10 the text did not automatically wrap.

Add flex-shrink so that it will
collapse if necessary.

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In preparation for making some substantial changes to this piece of
code, I'm translating it to JS.

In preparation for making some substantial changes to this piece of
code, I'm translating it to JS.

Use postcss and the autoprefixer plugin to post-process
CSS to add vendor prefixes and remove use of compass
mixins which did the same thing.

This moves compatibility concerns out of our styling
and down to a post-processor whose options can be adjusted
as necessary and moves us a step towards removing the
build dependency on compass.

Looking at the generated output, it fixes several issues
where we were inconsistent about which prefixes were used.

Pyramid webassets does have an autoprefixer filter but
it was written for an older version of autoprefixer which
was a standalone tool rather than a postcss plugin. In future
this also paves the way to replacing the cleancss asset filter
with an optional step in the postcss-filter.js script.

Consolidate .gitignore files

Auto re-install Python, Node deps if out of date

Having these scattered about across the repository makes it hard to work
out where something is ignored, and most tools/editors that read
.gitignore files don't pay attention to those not in the repository
root.

T87 - Improve group scope dropdown ui

For IE 10 and Safari < 9 support, use prefixed flexbox.

For now, this duplicates the flexbox declarations as is
done in topbar.scss. I will look into using autoprefixer for
this separately.

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cf410d0 broke standalone annotation pages by changing
`threadRoot.children` from an array into a thread container.
Unsurprisingly, `children` is supposed to be an array.

 * Use the singular 'groupList' everywhere

 * Simplify the logic for stopping click propagation
   when toggling the selected group

 * Remove underscore prefix for Controller classes as per the PR
   discussion.

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Fix detection of PDF URIs

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*N.B.* This does not fix the underlying problem, but it does make it
possible to deploy the existing codebase without breaking everything in
production.

70c9b9b broke a number of features of the h client that were toggled on
for PDF documents, by renaming the Annotator PDF plugin from
`Annotator.Plugin.PDF` to `Annotator.Plugin.Pdf`.

While it's certainly an ugly side-effect of a straightforward rename,
the problem is that `Guest#getDocumentInfo` (to pick one example) used
`@plugins.PDF?` to determine whether to use the PDF metadata
(provided by the PDF.js `PDFViewerApplication`).

In the absence of PDF metadata, `getDocumentInfo` falls back to using
`window.location.href`, which explains the behaviour identified
in #2506.

Fixes #2506.

Add a test for the controller part of the <groups-list> directive.

We have a couple of different patterns for testing directive
controllers in the code, the approach taken here follows the privacy
dropdown's directive in simply exporting the controller's constructor
as a 'private' export and referencing it directly in the test.

 * Rename the exports in the 'directive/privacy' module for consistency

 * Restructure the 'New group' item to make icon
   and label align with the items above it

 * Make the whole 'New group' section clickable

 * Make 'New group' icon bold for visual consistency
   with other icons

 * Use the prerendered group URL from the API instead
   of generating it locally

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 * Use an element directive for <group-list> for
   consistency with the <privacy> directive and because
   the directive has its own template.

 * Use flexbox for easier layout of items in the groups
   dropdown list.

 * Update the hover and selection states of items in the dropdown
   list as per the mocks.

 * Add descriptive titles to all links in the list

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 * Use the brand color for hovered items,
   including selected items.

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Use nesting for readability.

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Use a light grey background.

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Add make target to run karma tests with auto-watch enabled

Show orphan annotations with a notice

The positions of the anchors are no longer needed.