Long story short version. Took your advice and tried calling geany from command line without plugins.
Lesson learned: the filetype .md is recognised as part of the core functionality - no plugins needed.
Uninstalled all plugins and uninstalled geany. then installed both from mint software source. - no change in behaviour.
Established file location for plugin libraries on my system and noted that markdown was not installed.
The web page for markdown suggests contacting the geany team which is why I made this original call.
However it also give the author's email address (Matthew Brush at geany.com) so I will follow up with him.
It is slightly misleading having the web page up but no libraries installed.
As an aside I have found a python library that converts markdown to html so I can(hopefully) write a script to invoke this when the execute command is called

Thanks again

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