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From Omni support:

The path those plug-ins need to be places is a little complicated now that OmniOutliner is 'sandboxed'. Let me know if you have any trouble getting to this location:

Home Folder → Library → Containers → com.omnigroup.OmniOutliner4 → Data → Library → Application Support → The Omni Group → OmniOutliner → Plug-Ins

then the file name itself should be Markdown.ooxsl. (You may need to create the 'Plug-Ins' folder, be sure that's spelled correctly or OmniOutliner might not be able to read from it correctly.