Fix index page for files/ott, fix api host for D3 tree views
Merge branch 'master' into ott-index-page

Conflicts:
	deploy/files.opentreeoflife.org/other/synth_viz_dyn.html
	deploy/files.opentreeoflife.org/other/taxa_viz_dyn.html
Merge branch 'ott-index-page'

Fix index pages and API host for D3 tree views.
Fix missing search-context list on Contact page.
Add UI for choosing from mapping options

Addresses #407. This provides exact-match-only "quick mapping" and more
intense "careful mapping", which includes approximate matches and offers
a choice to the curator. Currently the choice is automatic: bulk mapping
is always quick, single-taxon mapping is more careful.
Merge pull request #408 from OpenTreeOfLife/improved-otu-mapping

Add UI for choosing from mapping options
Explain our latest conventions in sample.config

This shows and documents our current practices for defining the API
server(s) and using scheme-relative URLs.
Change /bin/sh to /bin/bash in push.sh
Disable ssl (in apache) if certs aren't found
Merge branch 'master' of github.com:OpenTreeOfLife/opentree
Move shared apache config out of sites-* folders
Remove unwanted MSIE exceptions in apache config
purge deprecated curnewicks
Protect uploads/ from being tracked/clobbered.

This is where we store uploaded files on production. It should be
ignored by git, as we've done in the main webapp/.gitignore
Merge branch 'master' into Cavia

Conflicts:
	curator/views/study/edit.html
	deploy/push.sh
	deploy/sample.config
	deploy/setup/apache-config-vhosts