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While I know I can annotate within a map, what is being used for documenting your work:sources of data, choices of color/per layer with each map made ( thinking along the lines of templateing, so as not have to deconstruct a map after the fact ).

laundry list of what makes up the map, font selections, color choices.

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I think it's best to keep as much information as possible embedded into the map itself. This way if someone happens upon the data absent supporting documentation, they always have a means to understand it's context.

In QGIS, it seems there is a "metadata" section in the map properties. Access it by:

right-click on the layer > properties > metadata

here you can give the map a title and "abstract". I would use this field to document all the items you mentioned, but specifically would include:

  1. data sources
  2. method used to compute the map
  3. additional information/references needed to understand the context of the map.
  4. MOST IMPORTANTLY: your name/contact information.

In GRASS, a comment is automatically added to every map that describes the method used to compute the output image. It's a start, but in general metadata is invaluable.

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