Add progress bars to pipeline instances table on dashboard.

refs #2006

Conflicts:
	apps/workbench/app/assets/stylesheets/application.css.scss
Fix up job/pipeline progress bars on dashboard.
Fix progress bars on pipeline_instances#show
Expand graph border to tab pane width.
Remove extra breadcrumb separator in "no breadcrumbs" mode.
Use .badge-alert to highlight notification badges.
Clean up collections index and show->files tables.
Highlight "Dashboard" instead "Users" in left nav when on
dashboard. Also bring back "System" nav links.
Rearrange thread_with_api_token around_filters so current_user is
available even when using thread_with_optional_api_token.

This makes notifications show up on users#home when accessed via root
url.
Remove extra divider in notifications list.
Fix up pipeline_instances#index and #compare.
Fix up collections search box on dashboard.
Fix up collections#index search box with bootstrap3 styles.
Fix up tab titles.
Add space under tab row.
Add section headings to API examples.
Merge branch '1979-workbench-ui-TC'

refs #1979
refs #1976
closes #2005
closes #2006
refs #2008