docs: Use envvar directive to attach semantics

Among other things, this makes the var names linkable with

    :envvar:`…`

and indexes them not just individually but also collectively under
"Environment variables" so the index includes a single list of all
documented vars.

When I originally wrote this page, I didn't yet know about the envvar
directive and role.  I've since used it extensively in Nextstrain CLI's
documentation, though.

augur/utils.py

@@ -104,7 +104,7 @@ def write_json(data, file, indent=(None if os.environ.get("AUGUR_MINIFY_JSON") e
     file
         file path or handle to write to
     indent : int or None, optional
-        JSON indentation level. Default is `None` if the environment variable `AUGUR_MINIFY_JSON`
+        JSON indentation level. Default is `None` if the environment variable :envvar:`AUGUR_MINIFY_JSON`
         is truthy, else 1
     include_version : bool, optional
         Include the augur version. Default: `True`.

docs/usage/envvars.rst

@@ -5,13 +5,15 @@ Environment variables
 Augur's behaviour can be globally modified by the values of some specific environment variables.
 These can be especially useful in the context of an entire pipeline or workflow which uses Augur, as the environment variables can be set once for all Augur commands at the start of the pipeline.
 
-``AUGUR_MINIFY_JSON``
+.. envvar:: AUGUR_MINIFY_JSON
+
     Boolean.
     If set to a non-empty value, all JSON output produced by Augur will be minified by omitting indentation and newlines.
 
     Minifying the JSON will substantially reduce file sizes, which is helpful for large, deeply nested trees.
 
-``AUGUR_RECURSION_LIMIT``
+.. envvar:: AUGUR_RECURSION_LIMIT
+
     Integer.
     If set to a non-empty value, the Python recursion limit will be set to the given value early in Augur's execution by calling :func:`sys.setrecursionlimit`.