Cleaning up base.pm

Better, cleaner warnings in tests.

Fixes for bug 3381.

Versioning added

Fixed formatting to conform to Bioperl style recommendations.

BioPerl-Run release 1.6.900

sync with trunk

svn path=/bioperl-run/branches/branch-1-6/; revision=16221

merge last commit to branch

svn path=/bioperl-run/branches/branch-1-6/; revision=15575

bump version

svn path=/bioperl-run/branches/branch-1-6/; revision=15567

sync with trunk

svn path=/bioperl-run/branches/branch-1-6/; revision=15521