In each MD I create, I include a standard Markdown metadata block (based on Calibres' implementation of the Markdown 'Meta' extension) and an initial "# title / ##### source" pair. Having this inserted into each "empty" file created would save that typing/cut-n-paste.
In general, being able to custom template the contents of each new "empty" file, would be fantastic. Calibre already seems to do some of this, i.e. the empty ePub comes pre-formatted with title, etc. Additionally, starting off the content-creation process without having to stare at an ACTUAL BLANK FILE provides a small psychological boost *grin*.
Thanks for the heads-up on the .opf. I'll have to go explore that !
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