Updated config for metazoan species
added option $filename for get_FTP
if filename is specified, will save source to file rather than in an array
good for big downloads
Automatic merging of dev into master

* dev:
  added option $filename for get_FTP if filename is specified, will save source to file rather than in an array good for big downloads
After git move functgenomics is now funcgen.

Thanks to Nathan and Gareth for pointing this out. Due to the Git migration
we now have to use ensembl-funcgen for the regulation checkout.
when removing features, update meta_coord accordingly
if this is the last feature of its kind, delete corresponding meta_coord entry
if it was the longest feature of its kind, update meta_coord to second longest feature
added remove method for coord systems
added method remove_assembly
when running remove method, run _pre_remove method to update meta_coord table
no need leaving unliked entries
when removing slice, remove any attached assembly entries
Automatic merging of dev into master

* dev:
  no need leaving unliked entries when removing slice, remove any attached assembly entries
Remove read coverage support

The read_coverage table and its API support are being removed
from the variation API; remove calls to these API components
and remove references from code docs
allowing multiple mappings for lrgs, because they are a special case
INSERT replaced by INSERT IGNORE
if attribute already exists, not need to scream warnings
[ENSCORESW-797]. Update to refer to the new Ensembl Git repos instead of CVS modules.
[ENSCORESW-797]. Download table.sql for different releases from GitHub.
update attrib_type table, using longer varchar for 'code' column
Automatic merging of dev into master

* dev:
  update attrib_type table, using longer varchar for 'code' column
missing apache2 licence in some patch files
[ENSCORESW-812]. Better table saving.

Due to changes in BaseFeatureAdaptor we need to save the state of
meta_coord otherwise a number of tests will begin to fail. Same is
true of xref.
We need to call coord_system. No method exists called cs()