allow custom config overrides only if flag queries is not the default value

Author: klujanrosas

packages/apollo-cli/src/load-config.ts

@@ -59,7 +59,7 @@ export function loadConfigStep(
         };
       }
 
-      if (flags.queries && (!ctx.config.queries || ctx.config.queries.length == 0)) {
+      if (!ctx.config.queries || ctx.config.queries.length == 0) {
         ctx.config.queries = [
           {
             schema: "default",
@@ -68,6 +68,13 @@ export function loadConfigStep(
           }
         ];
       }
+      else if (flags.queries != '**/*.graphql') {
+        ctx.config.queries = ctx.config.queries.map((query: any) => {
+          return Object.assign({}, query, {
+            includes: flags.queries.split("\n")
+          })
+        })
+      }
 
       if (flags.key) {
         if (Object.keys(ctx.config.schemas).length == 1) {