Preserve metadata in more places (#12848)

# Description
This PR makes some commands and areas of code preserve pipeline
metadata. This is in an attempt to make the issue described in #12599
and #9456 less likely to occur. That is, reading and writing to the same
file in a pipeline will result in an empty file. Since we preserve
metadata in more places now, there will be a higher chance that we
successfully detect this error case and abort the pipeline.

crates/nu-command/src/filesystem/save.rs

@@ -322,7 +322,9 @@ fn saving_to_source_file_error(dest: &Spanned<PathBuf>) -> ShellError {
             dest.item.display()
         ),
         span: Some(dest.span),
-        help: Some("You should use `collect` to run your save command (see `help collect`). Or, you can put the file data in a variable and then pass the variable to `save`.".into()),
+        help: Some(
+            "insert a `collect` command in the pipeline before `save` (see `help collect`).".into(),
+        ),
         inner: vec![],
     }
 }