Make upgrade procedure consistent with respect to code, tools and data. Now each require an explicit flag to upgrade. Fix documentation to match new approach. Fixes #183
Fixed memoization for remove read number.

In the edge case where it was a memoized file the read numbers on
the end, it returned the wrong filename.
Finalize disambiguation by incorporating code from @mjafin into bcbio-nextgen. Documentation and testing in place
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen