add GenomeThreader paper to web site
make formatting more consistent
cosmetics
use common check for mandatory option
fix Ruby version for webapps to 1.8
Merge pull request #269 from satta/stuff

Minor website and cosmetics changes
add gt_visitor_stream_get_visitor()
add -retainids option to 'gt extractfeat'
update .gitignore
Merge pull request #271 from satta/retainids

add -retainids option to 'gt extractfeat'
make GTF parser more robust
Merge pull request #272 from satta/gtf-news

make GTF parser more robust
extend tidy mode in GTF parser
Merge pull request #273 from satta/gtf-news

extend tidy mode in GTF parser