Fix different_case check ordering

[acdha]

This fixes the problem mentioned in #119 by testing for case-insensitive filename conflicts before adding the lower-cased filename to the path Set.

[coveralls]

Coverage remained the same at 98.282% when pulling 6040c62ff82c7b794c13a28abb428d6631864930 on acdha:fix-different_case-check-ordering into 2b7002e62d721f5eb50461e4c4c70a6ef643ec1d on LibraryOfCongress:master.

[jscancella]

We should probably add a test for the linter that should not return any warnings to catch possible errors like this again in https://github.com/LibraryOfCongress/bagit-java/blob/master/src/test/java/gov/loc/repository/bagit/conformance/BagLinterTest.java