small improvements

[jmbuhr]

• docs: specify to call your logger kimmdy.<pluginname>
• logging of recipe steps should specify that it's an ix (0-based), not id
• fix analysing reactions results csvs that contain new custom functions
• analysis tools (trjconcat) do weird things
• should we accept np.int subtypes fore RecipeSteps as well instead of just int?
• general inconsistencies between xtc, trr, both
• plugin authoring: xtc = files.input["xtc"] vs xtc = files.input.get("xtc")... AutofillDict is very clever, but needs better documentation. Maybe too clever.