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look at old fashioned gene remarks as well as gene hidden remarks when identifying potential fragmeneted loci

  Only use the Config::IniFiles module if it is installed on the system.
  If it isn't, assume that the configuration is in the old style (piece
  of Perl code that is require'd).

  This code will break if the user *wants* to use the new ini-file style
  of configuration of the Registry but the Config::IniFiles module is
  not installed.

Tested.

ensembl-46'.

Sprout from master 2007-08-14 12:10:20 UTC Patrick Meidl <pm2@sanger.ac.uk> 'project to contigs instead of clones so that it also works for WGS regions'
Delete:
    misc-scripts/protein_match/process_pmach.pl
    modules/Bio/EnsEMBL/DBSQL/Clone.pm