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bugfix: default_insertion_method becomes INSERT (INSERT_IGNORE for Jobs only) to avoid masking FK collisions in mysql 5.6

* version/2.4:
  bugfix: $PWD/perl5 was incorrectly listed

* version/2.4:
  Added a test for the "take_time" parameter of Dummy
  Unneeded dependency
  Trivial test to complete the coverage of Bio::EnsEMBL::Hive::Version
  "prove" itself should not be listed in Coveralls
  Also test the dark collection
  Added tests for the remaining patterns
  Added documentation about the Params interface, and the changed made in 2.4
  bugfix: use varchar, otherwise Postgre pads the strings with whitespace

Sorting the values here is too difficult, so instead we ask Perl to make the sort stable, and we store the insertion order of the keys in the hash (which follows the collection)

To make generate_graph deterministic, we basically need to sort the values of each hash by their corresponding key

The time-complexity of find_one_by() is O(n)

added -dot_input flag to generate_graph.pl to optionally produce an intermediate .dot file that we feed into dot

use param("HIVE_semaphored_job_url") to point at the remote funnel, and make sure it is propagated correctly

general infrastructure change to perform all semaphored_job-related operations via the corresponding adaptor