Merge branch 'master' into Cavia

This moves lots of recent improvements to the current production branch.
Fix index page for files/ott, fix api host for D3 tree views

Conflicts:
	deploy/files.opentreeoflife.org/other/synth_viz_dyn.html
	deploy/files.opentreeoflife.org/other/taxa_viz_dyn.html
purge deprecated curnewicks
Merge pull request #411 from OpenTreeOfLife/ott-update-and-viz-fixes

Fix index page for files/ott, fix api host for D3 tree views
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
Move shared apache config out of sites-* folders
Remove unwanted MSIE exceptions in apache config
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 #413 from OpenTreeOfLife/search-on-contact-page

Fix missing search-context list on Contact page.
Changing button 'Map carefully' to 'Fuzzy matches'
Merge pull request #414 from OpenTreeOfLife/otu-mapping-quick-vs-careful

Add UI for choosing from mapping options (first attempt), for Cavia
Remove OPENTREE_API_HOST and related explanation.

This was not needed and confuses the documentation here, as pointed out
in
https://github.com/OpenTreeOfLife/opentree/commit/0688020bd4e5f03d97ad029ce8d2d8ce664dcaf7#commitcomment-7658480
Split HTTP vs. HTTPS vhost configuration.

See related discussion in #412.
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
Add the SSL vhost file (d'oh!)
Merge pull request #412 from OpenTreeOfLife/deployment-fixes

Deployment fixes for Cavia (production)
Merge branch 'master' into Cavia

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