run: ensure <analysis_directory>/config.yaml overrides workflow config

Because of the order in which Snakemake merges configs, we must also provide the 
user's config from their analysis directory to override workflow configs
provided via the `--configfile` option.

See detailed discussion in 
<#462 (comment)>

Author: joverlee521

nextstrain/cli/command/run.py

@@ -267,6 +267,15 @@ def run(opts):
     if workflow_configfile:
         resolved_configfile = resolved_pathogen / workflow_configfile.relative_to(pathogen.path)
 
+    resolved_overlay = None
+    if (opts.analysis_directory / "config.yaml").is_file():
+        resolved_build = (
+            docker.mount_point(build_volume)
+                if opts.__runner__ in {docker, singularity, aws_batch} else
+            build_volume.src.resolve(strict = True)
+        )
+        resolved_overlay = resolved_build / "config.yaml"
+
     print(f"Running the {opts.workflow!r} workflow for pathogen {pathogen}")
 
     # Set up Snakemake invocation.
@@ -296,6 +305,10 @@ def run(opts):
         *(["--configfile=%s" % (resolved_configfile)]
             if resolved_configfile else []),
 
+        # Ensure the overlay config in the user's analysis directory
+        # overrides any default config file provided above.
+        *(["--configfile=%s" % (resolved_overlay)]
+            if resolved_overlay else []),
         # Pass thru appropriate resource options.
         #
         # Snakemake requires the --cores option as of 5.11, so provide a