Defining the set of existing versions in a git repository with a function is done through traversal of several directories and collecting information into array @files. Data collection for each directory is the same, save for the directory name. The Perl instructions have duplicated by copy-and-paste.
Unfortunately, the @files array is redeclared in each block with the result that only the last assignment to the array is kept, effectively erasing previous collected data and losing the associated versions.
Suggested fix in lxr.conf template: declared only once array @files before the directory blocks and "unshift" the discovered versions into it instead of assigning the array.
Bug present since release 1.0.0