fix several bugs within wfbench (and a minor one for wfchef)

[jeff-yc-wong]

Major bugs

• sorted files by decreasing file_id lengh when renaming files to wfbench format to prevent partial/duplicate replacements (e.g. renaming a file call "input_01" before "input_01.txt")
• fixed bugs where inputs to the workflow (i.e. not produced by any task) is sometimes not generated due to only checking input files of root tasks

Minor bugs

• added a generate_json function, so then each translator wouldn't always write a workflow json in the current working directory when all it needs is the workflow_json obj
• made a change to pyproject.toml, since wfchef weren't being registered as an executable