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FYI you're command-line is incorrect. The nyc merge command requires a positional argument <input-directory> before [output-file]. That said even using the correct arguments results in an exception if the destination is a file in a non-existent folder so I've posted a patch for that.
Link to bug demonstration repository.
https://github.com/quasicomputational/nyc-merge-missing-parent
Expected Behavior
nyc creates the directory and writes to the named file.
Observed Behavior
Forensic Information
Operating System: Debian.
Environment Information: https://gist.github.com/quasicomputational/e423212b707fa2232d04b8dd7578bbf9
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