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The GAPI tools
don't have any dependency on gtk-sharp and should work for all bindable native libraries. Hence they should have their own repository and package. In fact some distributions already have GAPI-specific packages like "gtk-sharp3-gapi" in Debian-based ditros.
Aside from the conceptual justification for the split, GAPI would get more exposure, if it had its own repo. This is because bindings authors of any native library - gtk-sharp devs excluded - usually wouldn't anticipate GAPI being part of gtk-sharp and thus have difficulties in contributing improvements to GAPI.
Development and release management would also profit from a split: GAPI versions would not have to be tied to gtk-sharp versions any more and GAPI can thus have its own release cycle. GAPI developers can concentrate on GAPI development and don't have to account for the gtk-sharp build not to break.
I've created a gapi-sharp repsoitory here: https://github.com/antoniusriha/gapi-sharp and a pull request with the respective changes to gtk-sharp here: https://github.com/mono/gtk-sharp/pull/124