I don't like the idea of generating a source file to create alias symbols, just because the GIR generator tool can't be properly told to put those as methods of the object.

Can't you, instead of actually adding the symbols, trick the tool to understand what you want? Basically, rename the symbols it parses, and then fix them back in the output so they refer the actual name.

Maybe something roughly around those lines:

TEMP_HEADER=geany-gtkdoc-sciobjected.h

sed 's/sci_/scintilla_object_/' geany-gtkdoc.h > $TEMP_HEADER
g-ir-scanner ... $TEMP_HEADER
sed 's/cname="scintilla_object_/cname="sci_/' -i Geany-1.0.gir

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