This list would be shorter if you only examined the most recent version of each distribution.
For example, Bio::SeqIO::Fasta is from bioperl-0.05.1 (05 Jul 1999), while Bio::SeqIO::fasta is from bioperl-1.4 (23 Dec 2003).
Similarly, Petal::Hash::VAR is from Petal-0.64 (03 Sep 2002), while Petal::Hash::Var is from Petal-2.05 (05 Apr 2004).
In both cases, those modules are only used internally, so no public interface is broken by the case change.
Some of the other cases are still relevant -- for example, Stem and stem are from two different distributions.
If you wanted to make sure this didn't happen again, the PAUSE indexer could be patched to do case-folded comparisons so that module authors would be warned of this kind of conflict.
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