[fixes #40533665] Call body on response, not request
[fixes 40535747] correct setting user_agent
Ensure headers are set
[#40596389] Use joins rather than nester queries.
[#40535747] Hack Net::HTTP::ProxyDelta for our proxy

This initializer solves the issue seen with our corporate proxy
rejecting CONNECT requests by allowing the code to set additional
headers for the request.  It then sets the one header that is required
to stop rejection: User-Agent.

This is a nasty, nasty hack because it's a cut-n-paste of the connect
method from the JRuby 1.6.8 code, so if anything changes then this needs
to be updated.
Merge pull request #698 from JamesGlover/40533665_taxon_lookup_is_broken

[fixes #40533665] Call body on response, not request
Merge pull request #700 from mattdenner/40535747_issues_with_sample_accessioning

[#40535747] Hack Net::HTTP::ProxyDelta for our proxy
Merge pull request #701 from JamesGlover/40535747_issues_with_sample_accessioning

40535747 issues with sample accessioning
[#40596389] Remove comments
Merge pull request #702 from JamesGlover/40596389_inefficient_query_in_finding_sample_manifests

[#40596389] Use joins rather than nester queries.
[#40535747] Add remote file name to file uploads
Merge pull request #703 from JamesGlover/40535747_issues_with_sample_accessioning_b

[#40535747] Add remote file name to file uploads
[#40924463 migrates users table to InnoDB]
Merge pull request #706 from seandunn/40924463_migrate_users_table_to_InnoDB

[#40924463 migrates users table to InnoDB]
[#40764063] Add foreign key constraints
[#40764063] Rename migration to later date
[#40835189] Migrations to remove wrong entries
Merge pull request #708 from JamesGlover/40835189_remove_invalid_roles_users_entries

[#40835189] Migrations to remove wrong entries
Merge pull request #707 from JamesGlover/40764063_users-roles_relationship_is_causing_problems

40764063 users roles relationship is causing problems
[fixes #40605937] Ensure mysql output goes to console