* Don't load the Document plugin for PDF files; Annotator's PDF plugin
   provides the fuctionality (uri+metadata extraction) in these cases.
   Use async metadata extraction for PDF

 * Updated PDF plugin to fcdf1eac (pdf-update branch)

Close #1586

Only add the public principal to the annotation

We now wait until the annotation has been created and apply the
principal to the read array rather than overwriting the entire object.

Make replies public by default 

This fixes the annoying issue with replies defaulting to private
all the time.

Is bad. And IE doesn't like "initial".

Now allows permissions rules to be provided in the
beforeAnnotationCreated hook.

Add 404 page

Since the change to the stateless identity API we have not been
finishing the initialization when the user is not logged in.

Restore clearfix on form fields

This reverts the change in 8955140efeab69d0a88e3df69b59e21f6d394044.

Separate login errors for username and password

Prevent tag input field from changing height

Validate that email exists on forgot_password

Add a new simpler grid system.

This fixes an issue with floated columns failing to clear each other
when of different heights. We now use a flexbox implementation taken
from the Pure CSS grid system which fixes the whitespace inconsistencies
in Safari.

Improve math support for matrices, inline content and list item and block quotes containing math.

Add a third argument to the applyInlineMarkup() to handle inline math markup which uses both \\( and \\).

Delete the now unnecessary inlineMath() function, applyInlineMarkup() is now used instead.

Simplify scope.insertMath().

Splits up math and markdown rendering into 2 functions:

renderMathAndMarkdown handles blockmath, and renderInlineMath handles inline math. Multiline math like matrices is not supported with inline math, but this is ok because it wouldn't look right anyway.

This works around the nasty hacks involved in removing the whitespace
between inline-block elements without having to use comments or
negative letter/word spacing.

This does mean we can't do centered or right aligned grids very easily
at the moment. If we need these things in future we can reconsider.

This replaces the YUI module we had before and implements only the parts
of the system that we need at the moment leaving a far cleaner and more
readable api.

It's not currently used anywhere and we could do with a cleaner grid
implementation.

Username blacklist

Clean up code, add comments, and add CSS to hide MathJax rendered math in a collapsed annotation.

Since renderMath() is doing much more than just rendering math, it is now a part of ctrl.$render(). This commit also adds basic support for inline math. However, this is not quite ready, using inline math inside of lists or block quotes does not yet work.

The regular expression was incorrect and was matching the occurance of any backslash, but this commit fixes it as well as reintroduces the MathJax fallback.

Rewrites the renderMath() function to sanatize, render math, and render markdown.

Big thanks to @tilgovi for help here.