Update ProteinTrees_conf.pm

Added 'homoeologous_genome_dbs' for dealing with poplyploid genomes
Update EGProteinTrees_conf.pm

Added homoeologous_genome_dbs to deal with polyploid genomes
Update OrthoTree.pm

For homoeology pairs, don't only change the MLSS, but also the homology description.
Update EGProteinTrees_conf.pm

if division is plants, supersede the default 'taxlevels' parameter value.
Merge commit 'refs/pull/ensembl-github/12'

* commit 'refs/pull/ensembl-github/12':
  Update EGProteinTrees_conf.pm
  Update OrthoTree.pm
  Update EGProteinTrees_conf.pm
  Update ProteinTrees_conf.pm
Finalized the "homoeologous_genome_dbs" option

The files have been modified from the pull request:
 - homoeologous_genome_dbs is given to all ortho_tree* analysis
 - homoeologous_genome_dbs defaults to [] in the config files
Merge branch 'master' into feature/hmm_classification

* master:
  Finalized the "homoeologous_genome_dbs" option
  Update EGProteinTrees_conf.pm
  Update OrthoTree.pm
  Update EGProteinTrees_conf.pm
  Update ProteinTrees_conf.pm

Conflicts:
	modules/Bio/EnsEMBL/Compara/PipeConfig/Example/EGProteinTrees_conf.pm
"triticum_aestivum_d", not "triticum_aestivum_c"
bugfix: members returned would otherwise be lost in a local variable
safer to use the new rearrange-based call
allow some Locus members not to have fully defined dnafrag_ fields
do not occlude the generic Hive::PipeConfig::HiveGeneric_conf::pipeline_name() subroutine
Stable ID mapping is based on peptide IDs, not transcript IDs
New option for EG: not all the species have dnagfrags on master
Transaction in KTreeDist to make it resilient to failures
Getting closer to eHive 2.1 and its die/autoflow behaviour
New "cmd_max_runtime" parameter in GenericRunnable
ProteinTrees::MSA is now using RunCommand
It is safer to define a default value in the runnable
output_clusterset_id is defined at the pipeline level (not in the runnable)