File mappers by default won't match to these but if path_types includes "unstructure" or is set to "*any*" then such matches will be used.

The unstructured file mappers can include depth attribute on these matches - the default of "0" just stages the file itself, setting depth equal to "1" will stage the whole directory containing the file (though only the matching path will be rewritten in the job inputs), a depth of "2" will cause the whole parent directory of the file's directory to be staged, etc.... This depth feature should be useful when staging implicit index files used by various bioinformatics tools.

Updated the PathMapper and ClientJobDescription so that Galaxy should be able to be instrumented build and pass along these files during tool evaluation when write_parameters is false - though only this default path rewriting variant has been implemented and tested so far.

Additionally, LWR server side changes have been made to support this feature and unit and integration tests are included.