I love the migration to github, I love the big repo, and in particular I love that we now have a process for the cufflinks additions and the bowtie fixes! This isn't meant to backtrack on that - but actually move the idea forward even a step more.

If these tools are going to see a lot of activity (seems a reasonable assumption) moving them to their own repository would allow us to use planemo's Travis integration to pre-test pull requests and ensure things stay green before they even hit the test toolshed. (Here is an example of the Travis integration for bwa-mem - results here). It is very much modeled after @peterjc work on this.

There are a lot of downsides - it means decreased visibility for these tools in a way (or would it increase it) - less prestige I guess related to pull requests at least. The other downsides is everything we said about it being nice to grep through all of these tools at once, etc... - it diminishes tools-devteam to take some of the highest profile tools out of it.