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mvdbeek
8144e81107
Composite datatypes (e.g. pbed/Rgenetics) name their extra files via a "%s" -> base_name substitution, so tools can reference canonical paths like $input.extra_files_path/RgeneticsData.bed. In _fetch_target the resolved display name was written back into metadata["base_name"], which since the name-precedence change clobbered base_name with the dataset display name (for tool tests, a generated _COMPOSITE_RENAMED_* string). Composite files were then staged under the wrong names and tools relying on the canonical name failed with dangling symlinks. Decouple the two: keep respecting an explicitly provided display name, but leave base_name at its provided/default value so the canonical substitution is preserved. Also layer provided metadata over the datatype defaults instead of using one or the other. Adds a composite_pbed framework tool that references the canonical RgeneticsData.* names as a regression test. Fixes #22786