ColumnChooser: not all features_loaded messages are for our columns…

…such as OTF. Fixes RT 377142.
change dist/conf/client_ensembl_version to suit Git

requires team_tools:otter/79
Fetch/BigWig.pm: score the mean value in each bin, not the total.
Bio::Otter::Git - push globals into methods

%$commands is hidden
  behind two methods,
  inside a block

$cache_template is wrapped
  behind a method
  also hide the POD-to-be from parsers

$dir is hidden behind a method
Bio::Otter::Git - minor changes

make create_cache public method
  prepare to do it later, to avoid a version-lock
  lose one nocritic

error check on printf $cache_h

comment on ->dump
Bio::Otter::Git - stash also dist/conf/*

so we can obtain dist/conf/feature_branch after install
  but feature branches come from Git not dist/conf,
  I was confused...  but now the code is written and the info is useful

add another type of "param" value
  push old shell-command type into method
  define new type for dist/conf/*

->dist_conf method to access the values later

->dump not extended to report dist/conf/ in logfiles
  because the commitid is enough to recover it
Bio::Otter::Git - record feature branch

when run or built from dev, notice feature branches
display this in logfile and for "About..." box
Bio::Otter::Utils::About - show extra info

show parts of dist/conf in About box
Bio::Otter::Git - critic fix
Fetch/BigWig.pm: give the feature class a proper constructor (quietens "perlcritic --harsh").
Fetch/BigWig.pm: move the feature class to its own file.
Fetch/BigWig/Feature.pm: usr proper attribute code.
Bio::Otter::Git - POD for public interface
Bio::Otter::Git - importable tag :server_ensembl

makes the appropriate server-side Ensembl API available on @INC

this can replace the hard-wired numbers in scripts/apache/
  but those scripts still have to find otter$NN
  before they can call this
scripts/apache/* - unhardwire (server) ensembl version

take it from Bio::Otter::Git->dist_conf

  perl -i -pe 's|\Quse SangerPaths qw{ core bioperl123 ensembl\E\d+ (.*)|use SangerPaths qw{ core bioperl123 $1\nuse Bio::Otter::Git qw{ :server_ensembl };|' scripts/apache/*
B:O:L:Client - add feature branch to url_root

clients built from a feature branch
  extend their url_root to require Otter Server with matching feature

also requires team_tools.git 312365662c5602780515cde5e8774534533ec5f2
  to put the Otter Server in the correct place
Bio::Otter::Git - importable tag :match

to check we have matching Bio::Otter libraries

Otter::Paths will set $Bio::Otter::Git::WANT_MAJ_FEAT
  since webvm.git 00ac41d2f3b0c396d6a12e154ddf35e735ff6d0c

scripts/apache/* can call this to avoid mismatch

client side does not currently use this,
  the PERL5LIB is set up by assorted shell scripts
scripts/apache/* - unhardwire otter version

after finding it with Otter::Paths,
  ask Bio::Otter::Git to check that we got the right (major, feature)

requires Otter::Paths of webvm.git 00ac41d2f3b0c396d6a12e154ddf35e735ff6d0c


modified with
  perl -i -pe 's|(\Quse SangerPaths qw{ core bioperl123 otter\E)\d+( .*)|$1$2|;  s|(Bio::Otter::Git.*) };|$1 :match };|' scripts/apache/*
B:O:SA:Test - show details out of Bio::Otter::Git
Lace/Defaults.pm: default to GFF3.