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Sinlge Makefile, and it's hard to work with it #3

@cmllezr

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@cmllezr

Idk if the sinlge makefile is a bug of application-ontology template, but so many things are hard-coded there, which should not be hard-coded.
Idk if it's still fixable or a new repo is required, but I'd really prefer separating universally applicable stuff in the main makefile and the ontology specific stuff in the ontology-makefile.

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