Rework the testing of an empty log file for better testing.

We can now mock just the Run#log method for better coverage.
Add tests for taverna credentials in env variable.

For completeness.
[TAV-512] Fix overzealous file extension restrictions for inputs.

This is due to Paperclip being a bit keen, so we just coerce it into being a bit
more relaxed with the extensions on plain text types.
Add an alert flash to the test layout.

Also fix the ReadMe info about flash messages.
Use flash[:alert] not flash[:error].

flash[:error] is non-standard in rails 3.
Recover from failed run creation more gracefully.

Now redirects back to the run form do not die horribly.
Merge branch 'next'

* next:
  Recover from failed run creation more gracefully.
  Use flash[:alert] not flash[:error].
  Add an alert flash to the test layout.
  [TAV-512] Fix overzealous file extension restrictions for inputs.
Merge branch 'master' into list-inputs

* master:
  Recover from failed run creation more gracefully.
  Use flash[:alert] not flash[:error].
  Add an alert flash to the test layout.
  [TAV-512] Fix overzealous file extension restrictions for inputs.
  Add tests for taverna credentials in env variable.
  Rework the testing of an empty log file for better testing.