switch_to_puma
Remove Trinidad daemon gem
Override java proxy settings

Changes in jruby 1.7 include using jvm proxy defaults.
Unforunately it seems to ignore the noProxyHost settings.
If we overide the settings we can mimic the original
behaviour.
Override the Capybara Server and use in tests
Tweak script/server to use puma
Kill server threads with close
Puma 2.2.2
puma 2.3.3
[#61651832] Remove redundant controllers
[#61651832] Move documents controller
[#61651832] Remove request types administration
[#61651832] Remove submission workflows management
[#61651832] Repair user search
[#61651832] Prevent deletion of plate purposes
[#61651832] Remove unused study/documents actions
[#61651832] Delayed job routes and remove redundant links
Remove and refactor sample destruction/move
Merge branch 'production' into 61651832_remove_redundant_code
Remove unwanted tables
Merge remote-tracking branch 'sanger/production' into 61651832_remove_redundant_code