I have run into two issues on trying to produce a markdown report using a merge template.
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I used the “Generate Sample Report in Markdown” command which creates a “sample report template.md” file. The first line of the file is “<?output "report.md"?>” But on selecting the report from the Collection’s toolbar, no output file called “report.md” seems to be generated. The output does get displayed in a Notenik window called “Query Output” though. The same thing seems to happen with reports in HTML.
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After creating and renaming reports, if I create a query and save it, then the previously saved reports disappear from the dropdown menu in the Collection toolbar. The template file is still present in the reports folder. When I delete the query related files from the reports folder, the report reappears as an option from the dropdown menu.