[DOC] add new usage examples from the wild
tweak README
remove extraneous header tab
fix most filetype issues. intersect still raises error with empty files.
Merge converted to PFM, first check-in
[ENH] all shuffle with -incl to follow data distribution
[TST] run shuffle tests.
Handling empty files with headers
Merge remote-tracking branch 'upstream/master' into merge
Merge branch 'master' of https://github.com/nkindlon/bedtools2
Fixed merge conflicts
Unit tests and bug fixes for merge release
Merge branch 'merge'
Final unit tests for merge, including stranded merge bug fixes.
Merge branch 'merge'
Merge pull request #53 from nkindlon/master

Merge converted to PFM, first check-in
allow merge -d to have negative values for minimum overlap.
add missing help menu items (-S -header) to merge
cleanup KeyListOps help formatting
cleanup unit tests.