Pass --all-files explicitly so it is retained

In the lint workflow, passing extra-args replaced --all-files,
rather than keeping it but adding the extra arguments after it.

(But --show-diff-on-failure and --color=always were still passed.)

.github/workflows/lint.yml

@@ -15,6 +15,6 @@ jobs:
 
     - uses: pre-commit/[email protected]
       with:
-        extra_args: --hook-stage manual
+        extra_args: --all-files --hook-stage manual
       env:
         SKIP: black-format