Merge pull request #6 from jstalker/bwa_index_version

Bwa index version
FrontEnd->ask_question has new option strip_leading_trailing_whitespace, used by vrpipe-setup to avoid common user error; vrpipe-setup --cleanup also now tries to delete the withdrawn dataelement itself
when coercing str to dir/file we now strip trailing and leading whitespace. coercions from ArrayRef removed, since they surely never worked, and do not seem to work now
new --defunct mode for vrpipe-server
add option to $file->lines method to get the raw number of lines in the file
another change to fastq_merge_and_index to fix speed issues
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into develop
to increase speed, no longer causes a datasource prepare
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into develop
small optimisation in query to get uniuiely ours stepstates
added back (improved versions of) ArrayRef coersion for files and dirs so Base.t will pass, but there is still a problem with using arrayrefs when creating VRPipe::Files
updated to schema 24
added notes for 0.106
version bump
Merge branch 'release/0.106'
Merge branch 'release/0.106' into develop
resolve conflict from merge from develop
to avoid problems when testing, in deployment testing mode we no longer chdir when daemonizing and we force t and modules into lib during dispatch_vrpipecode()
renamed the has_many method in VRPipe::Pipeline from steps to stepmembers, which is now no longer used; we use step_members instead
we now include t in the lib, so the server can load test pipelines and steps