Add header menu spacing for markdown cells

fixes #449
Handle input menu when collapsed
Fix #353, handle server disconnects on client(mainapp).

When server disconnects, there will be a dialog prompting the user
about server has disconnected and asking to save the notebook
as a file on the client side. If user chose not to, the dialog is
dismissed and beaker starts hijacking keypress events to prompt the
same dialog again on such events. The dialog can also be opened by
clicking on the red 'offline' label on the nav bar.
Handle when the notebook is the root section

fixes #475
Merge pull request #481 from twosigma/sjs/475

Handle when the notebook is the root section
Merge pull request #480 from twosigma/alee/fix-353-freeze-when-offline

Fix #353, handle server disconnects on client(mainapp).
wait until websockets in the ipython kernel are ready before sending the initialization code over them.  fix Issue #478.
Merge pull request #476 from twosigma/sjs/449

Add header menu spacing for markdown cells
Merge pull request #482 from twosigma/spot/478

wait until websockets in the ipython kernel are ready before sending the...
Fix file open dialogs regressed in a4146e8
Fix menu gap in header
Update favicon location

fixes #450
Merge pull request #488 from twosigma/sjs/450

Update favicon location
Merge pull request #487 from twosigma/sjs/484

Fix menu gap in header
Merge pull request #483 from twosigma/alee/fix-file-open-dialog

Fix file open dialogs regressed in a4146e8
Merge remote-tracking branch 'origin/master' into alee/fix-267-evaluatejobmanager
Fix an issue about cancelling evaluation in evaluatejobmanager