Fixed wrong command in web_name_patches config
EG's PairAligner inherits from Ensembl's version

Only one file contains the pipeline structure. Both files define their
own parameters / memory requirements.
Print the debug in debug mode only
Various fixes
Added more doc
GenomeDB::species_tree_node_id() should be private
Fixed the path to the eHive doc
gene_align fields were not loaded
The GeneTree::alignment() is cached
Reuse the list of members
Fixed the doc
Efficiently copy all the sequence-related fields
bugfix: alignment format in dumpAlignedMemberSet()
Refactor the split_genes code

Among all the changes:
 - no need to define _tmp_name on the leaves (seq_member_ids are used instead)
 - the input tree is modified alongside the alignment
Fixed parsing of hmmemit's output
"fasta" is the default alignment format
Fixed the inheritance path
dumpTreeMultipleAlignmentToWorkdir() refactoring

dumpTreeMultipleAlignmentToWorkdir() and dumpAlignedMemberSet() had very
similar roles, and all functionnalities are now in the the first one.
Merge branch 'master' into feature/hmm_classification

* master:
  GenomeDB::species_tree_node_id() should be private
  Added more doc
  Various fixes
  Print the debug in debug mode only
  EG's PairAligner inherits from Ensembl's version
  Fixed wrong command in web_name_patches config

Conflicts:
	modules/Bio/EnsEMBL/Compara/RunnableDB/GeneTrees/GenericRunnable.pm
	modules/Bio/EnsEMBL/Compara/RunnableDB/ProteinTrees/NJTREE_PHYML.pm
Refactored the part that interprets TreeBest tags

The code to replace TreeBest tags with the Compara ones is cleaner. We now
start with an empty hash and add all the tags. Finally, we push everyhting
to the database with sync_tags_to_database(). Previously, the hash-tag was
left in a state with both kinds of tags.