Snakefile.genome/refine: Add comments on root_strain

Adding some comments to clarify the `root_strain`.

Thanks @genehack for calling out the magic-number¹
We will probably want to refactor the workflow to pull out these types
of values into a config YAML at some point, but I'm punting on that
for now.

¹ <#40 (comment)>

Snakefile.genome

@@ -173,6 +173,8 @@ rule refine:
         coalescent = "const",
         date_inference = "marginal",
         clock_rate = clock_rate,
+        # Using the closest outgroup as the root
+        # Make sure this strain is force included via augur filter --include
         root_strain = "A/skunk/NewMexico/24-006483-001/2024"
     shell:
         """