Update toy data results

Add Nickel to gut medium

Nickel is part of the biomass for archaea.

Fixes #232

updated version number again

added model test mode

- `gapseq test-long` reconstructs a model of E. coli, including all
  of gapseq's substeps. the resulting model is functional core model
- model test mode should run in 5-10min

Full model is constructed now *on the fly*

This change makes the binary file `dat/full.model.RDS` obsolete.
Finally...

`gapseq test` now also checks if full model can be constructed on the
local machine.

added emplate autotrophic medium for gapfilling

- refers #41

minor database updates

- added new compound which is used in reactions but not described yet
- some new bigg <-> seed exchange mappings

Small cleanup

Added a second version of the Bifidobacterium shunt

..., which utilizes the reaction 5.4.2.11 instead of 5.4.2.12