Deal with URLs and branding

Change 'dev' to 'api' in URLs (since 'dev' doesn't work; 'api' works for reading but is not being updated) and change 'API' to 'Phylesystem API' in running text to emphasize that this is only one component of the larger open tree suite.
Merge branch 'master' into treesource
Tweak URLs for repo to match current name
Merge pull request #91 from OpenTreeOfLife/prod-setup

Tweak URLs for repo to match current name
indentation
Merge branch 'master' of github.com:OpenTreeOfLife/phylesystem-api into treesource