Thanks for the reply and the tips. 

Just add another small tip to this thread: 
`-Q`/`-q` skips ELPA load path. So we need to manually add the ELPA load path to the debugorg.el. It looks like that by default the ELPA org-mode load path is ~/.emacs.d/org/$DATE


On Fri, Jun 6, 2014 at 10:57 PM, Thorsten Jolitz <tjolitz@gmail.com> wrote:
Achim Gratz <Stromeko@nexgo.de> writes:

> Nick Dokos writes:
>> I did that in the past (presumably for reasons similar to Thorsten's)
>> and I don't bother any longer (overriding is simple enough as you point
>> out), but the question  still bugs me: what's so bad about it?
>
> The reason it is bad is that parts of the code have already leaked out
> from the org/ directory via custom-load and autoloads and that's going
> to break things in the least convenient moment – for instance when you
> try to hunt down bugs via "-Q".  There simply is no way to remove the
> builtin Org from Emacs other than at build time and it's best not to
> pretend otherwise.  Some day Emacs might actually treat its built-in
> packages as actual packages so that you can de-activate or replace them,
> but I wouldn't hold my breath.

That sounds reasonable enough, but somehow that least convenient moment
never happens, while I remember *many* such moments when I still had more
than one Org on my machine ... but maybe I just don't huntdown bugs via
-Q often enough.

--
cheers,
Thorsten