Hi Don,

this is on purpose.  Putting a comma in front of such lines makes sure  
Org does not consider them as special, for example when searching for  
in-buffer options like #+STARTUP.  The same thing happens for lines  
startin with a star, which Org could mistake for an outline heading.
The parsers for startup options and for outline structure do not waste  
time on analyzing the structure of the document to distinguish lines  
inside and outside code blocks.

The commas admittedly look not so good in the Emacs buffer, but they  
will be stripped for editing with C-c ', and also for export.

Hope this explains it.

- Carsten

On Oct 4, 2008, at 4:17 PM, Womick, Don wrote:

> After running C-c ‘ (apostrophe) on a shell script between # 
> +BEGIN_SRC and #+END_SRC tags and returning to the org file using C- 
> c ‘ again, comments in the script have a , (comma) prepended.
>
> If I have
>
> #+BEGIN_SRC shell-script
> #! /bin/bash
> # some comments here... they'll be preceded by commas after C-c '  
> editing
> #
> ls
> cat myfile # inline comment here, isn't affected
> #+END_SRC
>
> and do C-c ‘ to pull it into an edit buffer, then C-c ‘ again to go  
> back to the org file, the result is
>
> #+BEGIN_SRC shell-script
> ,#! /bin/bash
> ,# some comments here... they'll be preceded by commas after C-c '  
> editing
> ,#
> ls
> cat myfile # inline comment here, isn't affected
> #+END_SRC
>
> Note the commas in front of each # (comment character).
>
> This seems to happen to # characters regardless of the editing mode…  
> I tried a Java snippet with the same results:
>
> Before:
>
> #+BEGIN_SRC java
> # hash comment
> // java comment here
> public class MyClass() {
>     private String myVariable; // inline comment here
> }
> #+END_SRC
>
> After:
>
> #+BEGIN_SRC java
> ,# hash comment
> // java comment here
> public class MyClass() {
>     private String myVariable; // inline comment here
> }
> #+END_SRC
>
> I’m running the following:
>
> Org-mode version 6.06b
> GNU Emacs 23.0.60.1 (i386-mingw-nt5.1.2600) of 2008-08-19 on  
> LENNART-69DE564 (patched)
>
> Thanks for org-mode… I’ve been using this amazing piece of software  
> almost as long as I’ve been using Emacs (a couple of years now).
>
> Regards,
> Don Womick
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