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
[#56276024] Add customer responsible flag
[#61616796] Avoid displaying stack trace to user.
[#61616796] Accessioning errors are more informative
[#61616796] Detect mismatched order options
Fix seeds
Repair broken tests
[#56276024] Add fail but charge to api interface
[#56276024] Add fail but charge to Sequencesape UI
Merge branch 'production' of github.com:sanger/sequencescape into 56276024_fail_but_still_charge_flag
Conduct tasks in trasaction
Resolve merge conflict
Resolve merge conflict