Finalizing the FBC version 3 specification

[bgoli]

Issues addressed in this PR (addresses #405)

• implemented the changes suggested in fbc v3: empty lists? #396 allowing empty LoUDC and LoKVP
• red text removed for a more soothing reader experience
• fixed an example that was not included properly
• added a, hopefully, final version of the spec as a PDF sbml-fbc-version-3-release-1.pdf

[fbergmann]

@bgoli thanks for getting this done, there are still some overflows into the margins, that would be great if we could remove them, worst of them are:

• url:

  sbml-specifications/sbml-level-3/version-1/fbc/spec/intro.tex

  Line 53 in c05d3ad

  \url{https://web.archive.org/web/20151006163154/http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/Flux_Balance_Constraints_Proposal_(2012)}

• page 21, line 16 and 25 'http://sbml.org/fbc/keyvaluepair'
• maybe the mailing list link.

[bgoli]

Thanks @fbergmann, good points I'll do an overflow check

[luciansmith]

Chiming in here so I know when this is merged, and I can email sbml-discuss.

[luciansmith]

There are still other things that need to be fixed, but none of us can actually fix them until this merge happens, because we don't have access to Brett's personal github repository. I'm going ahead and merging this so I can make other fixes and post to sbml-discuss before the JIB deadline.

[bgoli]

What is the status of the V3 specification is there anything else that needs to be done?

[luciansmith]

I think we're good! Sorry; I thought this was done for the last JIB issue. I merged everything into 'develop', and made a few final changes, mostly to the validation rules relating to the final open issues, including one commit I had made to the wrong branch (sorry). Everything else looks OK, I think. The JIB directory needs work, I think.