Greg Minshall writes:
- the next time i open the Org Src buffer, whatever lint-like process is
   running for that language may complain about extra spaces at the end
   of a line.  (does that mean my experience is different from yours, or
   at least from your expectation?)
If I try your original examples with `emacs -q' I do not get extra whitespace in the org src buffer. Those two spaces in the original org buffer -- that are due to `org-edit-src-content-indentation' -- are removed in the org src buffer. If
you do not find it to be the case, then I'm missing something.

Anyway, here's a patch that cleans up blank lines, except the current one. It
preserves the fix for the original issue.

Can you try it out ?

Regards,

--
Sébastien Miquel

>From 405c2be7487c564e72a9f01a940f96dc19ff16ad Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Miquel?= <sebastien.miq...@posteo.eu>
Date: Wed, 23 Jun 2021 15:25:58 +0200
Subject: [PATCH] org-src.el (org-src--contents-for-write-back): Do not indent
 blank lines

* lisp/org-src.el (org-src--contents-for-write-back): Do not indent
blank lines, except for the current line.

This was the original behaviour for all blank lines, before `857ae366b3`.
---
 lisp/org-src.el | 23 ++++++++++++++++-------
 1 file changed, 16 insertions(+), 7 deletions(-)

diff --git a/lisp/org-src.el b/lisp/org-src.el
index 79f002e56..faacb53e3 100644
--- a/lisp/org-src.el
+++ b/lisp/org-src.el
@@ -443,14 +443,20 @@ Assume point is in the corresponding edit buffer."
 		0))))
 	(use-tabs? (and (> org-src--tab-width 0) t))
 	(source-tab-width org-src--tab-width)
-	(contents (org-with-wide-buffer (buffer-string)))
-	(write-back org-src--allow-write-back))
+	(contents (org-with-wide-buffer
+                   (let ((eol (progn (end-of-line) (point))))
+                     (list (buffer-substring (point-min) eol)
+                           (buffer-substring eol (point-max))))))
+	(write-back org-src--allow-write-back)
+        marker)
     (with-current-buffer write-back-buf
       ;; Reproduce indentation parameters from source buffer.
       (setq indent-tabs-mode use-tabs?)
       (when (> source-tab-width 0) (setq tab-width source-tab-width))
       ;; Apply WRITE-BACK function on edit buffer contents.
-      (insert (org-no-properties contents))
+      (insert (org-no-properties (car contents)))
+      (setq marker (point-marker))
+      (insert (org-no-properties (car (cdr contents))))
       (goto-char (point-min))
       (when (functionp write-back) (save-excursion (funcall write-back)))
       ;; Add INDENTATION-OFFSET to every line in buffer,
@@ -458,10 +464,13 @@ Assume point is in the corresponding edit buffer."
       (when (> indentation-offset 0)
 	(while (not (eobp))
 	  (skip-chars-forward " \t")
-	  (let ((i (current-column)))
-	    (delete-region (line-beginning-position) (point))
-	    (indent-to (+ i indentation-offset)))
-	  (forward-line))))))
+          (when (or (not (eolp)) ; ignore blank lines
+                    (eq (point) (marker-position marker)))
+	    (let ((i (current-column)))
+	      (delete-region (line-beginning-position) (point))
+	      (indent-to (+ i indentation-offset))))
+	  (forward-line)))
+      (set-marker marker nil))))
 
 (defun org-src--edit-element
     (datum name &optional initialize write-back contents remote)
-- 
2.32.0

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