- rewrote fetch_by_stable_id*() methods to look up current versions of stable
  IDs in *_stable_id tables
- new method lookup_current() to assist the former (also replaces
  _lookup_version())
- new method add_all_current_to_history() to implement this behaviour for
  StableIdHistoryTree

- new methods to get properties of current db:
  - get_current_release()
  - get_current_assembly()

- fixed _resolve_type() to copy with non Ensembl-style stable IDs (e.g.
  Anopheles)

- removed deprecated methods

  - get_latest_StableIdEvent(): find latest Event in tree for a given stable ID
  - getters/setters for current db properties:
    - current_release()
    - current_assembly()
    - current_dbname()
  - is_incomplete(): flag to indicate incomplete trees

  - current_version(): retrieves current version of stable ID from db
  - is_current(): test if this is the current version
  - get_latest_incarnation(): get latest incarnation of stable ID from db
  - is_latest(): test if this is the latest version

- version() no longer lazy-loaded (now always set by adaptor)

- removed deprecated methods

as filled paragraphs.  Long lines shortened.  Spelling.

Make Vega transcript data URI a glob pattern.

directory before ls'ing.

Listings of subdirectories with 'ls' on FTP servers may return only
filenames *or* whole file paths.  This probably depends on the FTP
server software being used, but it makes relying on getting the whole
path back a bit silly.

all files are unchanged.

    The fetch_files() method returns a list of files, including
    directories where they can be found, so don't go prefixing them with
    $dir again silly.

All files are now treated as local, except for those configured as
'mysql:' URIs in the configuration file.

specific) file Seg_xrefs.txt of the IMGT/LIGM_DB and IMGT/GENE_DB
sources would clash.  Put the two files in subfolders.  Split the
sources.

--cleanup is specified on the command line.

Fetch uniprot.txt rather than swissprot.txt which does not exist on the
zfin.org HTTP server anymore.  Modify the ZFINParser accordingly (it
contains hardcoded file names) and use catfile() rather than manual
concatentation of file paths.

Add special source 'IMGT/LIGM_DB' (assumed to exist by SegmentParser,
but not explicitly connected with any species).

Collapse lists of data URIs by means of FTP file name globbing,
especially for the various RefSeq sources.

Updated some URIs to point to new data (e.g. FlyBase for Drosophila).

Make fetch_files() understand file name globbing for FTP transfers (will
not work for HTTP).

Make the command line switches --delete_downloaded and --cleanup work as
expected.

No longer mandatory to specify compara database on command-line; will use first one defined in registry file if not specified on the command line.

let a species have multiple 'taxonomy_id' entries, one for each strain.

Change anopheles configuration to comply to this.

Change Perl script to take care of this as well.

'xref_config.ini' using the 'xref_confg2sql.pl' script.

New key: 'strain_of' (used for anopheles strain).

*** HEADS UP ***

The xref_parser will now croak if used with the old
populate_metadata.sql file.

Make name2species_id() also consider aliases (this is currently comment
out).

Stub for fetch_file() method that will eventually handle downloading of
data.