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In org mode I use a german time format for timestamps

(setq org-time-stamp-custom-formats '("<%a. %d.%m.%Y>" . "<%a. %d.%m.%Y %H:%M>"))

For example <Fr. 25.06.2021>. Internally this is represented as <2021-06-25 Fr>.

So, I can for example isearch-forward for 06-25 to find the time stamp, but searching for 25.06. doesn't work.

Is there any way to configure emacs such that it works to useisearch-forward for a substring of the german time stamp representation?

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org-times-stamp-custom-formats affects the display of time stamps: it does not affect how the time stamp is stored in the file. isearch on the other hand does not care about how the display looks; it only cares about what's in the buffer.

So I believe the answer to your question is "no".

The custom time stamp format is implemented using overlays (do C-h i g (elisp) Overlays to read about them). You might be able to cobble up something using the functions described there, but I think it is going to be a fairly fragile thing.

Org mode really only supports the ISO time stamp format, so you are probably better off remembering that and using ISO format (sub)expressions for searching.

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