Deprecate the --apply-format-changes option of check/all (#7964)

And update the development doc with preferred `check/all` options.

Follow-up to #7962

Author: pavoljuhas

check/all

@@ -58,6 +58,9 @@ for arg in "$@"; do
             extra_ruff_args=( --fix )
             ;;
         --apply-format-changes)
+            echo "Warning: option '--apply-format-changes' is deprecated." \
+                "Please use '--fix' instead." >&2
+            echo >&2
             extra_format_args=( --apply )
             ;;
         -*)

docs/dev/development.md

@@ -252,11 +252,13 @@ set the Python path and configuration arguments for you and cover more use cases
     - Run all continuous integration checks:
 
         ```bash
-        ./check/all [BASE_REVISION] [--only-changed-files] [--apply-format-changes]
+        ./check/all [BASE_REVISION] [--changed] [--fix]
         ```
 
-        If `--only-changed-files` is set, checks that can will focus down to
+        If the `--changed` option is set, checks that can will focus down to
         just files that were changed (trading accuracy for speed).
+        The option `--fix` will apply safe corrections from linter and
+        formatter tools to address problems detected in the code.
 
 In the above, `[BASE_REVISION]` controls what commit is being compared
 against for an incremental check (e.g., in order to determine which files changed).