add note about after_script being run separately

doc/ci/yaml/README.md

@@ -95,6 +95,12 @@ be an array or a multi-line string.
 `after_script` is used to define the command that will be run after for all
 jobs. This has to be an array or a multi-line string.
 
+> **Note:**
+The `before_script` and the main `script` are concatenated and run in a single context/container.
+The `after_script` is run separately, so depending on the executor, changes done
+outside of the working tree might not be visible, e.g. software installed in the
+`before_script`.
+
 ### stages
 
 `stages` is used to define stages that can be used by jobs.