more portable pipeline + ending DOC tag fix

The biggest contributions here:

* Fixed bug in annotator (see https://github.com/fmof/anno-pipeline/commit/1ff61e3db9a4e715c872c823e6f08d6e2722073f#commitcomment-3421513)
* Pipeline modified to optionally parallelize via qsub
* removed hard path links
* Recaser (true casing) option added
* added Jonny's sequential submission script
* added sequential qsub wrapper
* added .gitignore

I recommend diffing with <tt>-w</tt>