Fix #628 and improve parameter reference error messages

[ThomasHickman]

This fixes #648 and makes the error messages for parameter references better (as referenced in the commit). I've also cleaned up the code which I've changed, to make it easier for other people to edit.

[cwl-bot]

Can one of the admins verify this patch?

[mr-c]

Jenkins, add to test list

[mr-c]

Jenkins, add to testlist

[mr-c]

Running this with the example file from #648 (comment)

$ cwltool --validate expr_fail.cwl 
/home/michael/cwltool/env/bin/cwltool 1.0.20180210112813
/home/michael/cwltool/env/bin/cwltool 1.0.20180210112813
Resolved 'expr_fail.cwl' to 'file:///home/michael/cwltool/expr_fail.cwl'
Resolved 'expr_fail.cwl' to 'file:///home/michael/cwltool/expr_fail.cwl'
Tool definition is valid
Tool definition is valid

[ThomasHickman]

^ is this unexpected output, or are you just verifying that this PR works?

[mr-c]

Thanks again @ThomasHickman !