If all your shapes are on a transparent layer you can use Alpha to Selection on the layer, to make one selection of all the shapes, then apply the Stroke Selection all in one go.
To automate this, software such as Photoshop has layer effects which can be applied non-destructively to a layer, so that when you paint on the layer it can apply an outer stroke automatically as you paint. Unfortunately GIMP doesn't have this functionality at the moment, although it might in future. Krita also has layer effects, perhaps you could try that. However, it should be noted that raster image editing software is not the best for this kind of work. Vector image editors such as Inkscape (which is free) or Illustrator (not free) can apply strokes and fills to vector shapes, as you draw them.
Here's a quick example using Inkscape