Beamer presentation with notes: navigation does not work properly and "destination with the same identifier" warnings show up

Question

I am refloating a long-standing Beamer problem and will put a good bounty to it, to see if we can all solve this problem once and for all...

I am following on a previous question I posted here, and an old post that never got a proper answer, and adding some more information and problems detected just recently.

The problems are related to the navigation links in Beamer presentations WITH NOTES.

1. If you try to show your notes on the left, navigation links on the top of slides just plain do not work.
2. If you do like I did and switch notes to the right, the links on top work.

BUT STILL WE RUN INTO THE FOLLOWING PROBLEMS:

• Links in the table of contents do not work at all.
• You get infinite amounts of the following warnings (one per slide):

destination with the same identifier * has been already used, duplicate ignored

I think this is a really big problem with Beamer, I do not know if it is a bug or it can be solved somehow...

Turning off the links is not an option; though we will remove the warnings, the main reason why some of us use Beamer is for the awesome navigation that takes us quickly to a slide in a big presentation during the questions round.

It would be of great advantage if the navigation feature could be used together with the ability to add notes next to the slides... In fact, I do not understand why this is not possible.

I gave up trying to add the notes on the left, so let's try to make everything work at least with the notes on the right...

With notes on the right, navigation links on top of slides work, but we still need to make navigation in table of contents work too, and get rid of those terribly annoying warnings.

This is a MWE to start playing with:

\documentclass{beamer}
\usepackage{pgfpages}
\setbeameroption{show notes on second screen=right}%better notes on right

\mode<presentation> {
    \usetheme{Singapore}
}
\begin{document}


\begin{frame}[plain]
    \titlepage  
\note{
    Notes for the title page
}
\end{frame}


\section*{Outline}
\begin{frame}[plain]
\frametitle{Outline}
    \tableofcontents

\note{
    Notes for the table of contents
}
\end{frame}


\section{Frame 1}
\begin{frame}
\frametitle{Frame with notes 1}
    FIRST FRAME CONTENTS

\note{
    Notes for the first frame
}
\end{frame}


\section{Frame 2}
\begin{frame}
\frametitle{Frame with notes 2}
    SECOND FRAME CONTENTS
\note{
    Notes for the second frame
}
\end{frame}


\section{Frame 3}
\begin{frame}
    \frametitle{Frame with notes 3}
    SECOND FRAME CONTENTS
    \note{
        Notes for the third frame
    }
\end{frame}


\end{document}

EXTRA BONUS POINTS IF YOU ARE ABLE TO MAKE NAVIGATION WORK IN HANDOUT FORMAT TOO, WHERE NAVIGATION DOES NOT WORK AT ALL! Just use:

 \documentclass[handout]{beamer}
 \usepackage{pgfpages}
 \pgfpagesuselayout{2 on 1}[a4paper,border shrink=5mm]
 \setbeameroption{show notes}

Answer 1

I added a bug report to the beamer issue tracker regarding the destination warnings: https://github.com/josephwright/beamer/issues/370.

Regarding links and toc one can only quote the documentation of pgfpages (in pgfmanual.pdf)

A word of warning: using pgfpages will destroy hyperlinks. Actually, the hyperlinks are not destroyed, only they will appear at totally wrong positions on the final output. This is due to a fundamental flaw in the pdf specification: In pdf the bounding rectangle of a hyperlink is given in “absolute page coordinates” and translations or rotations do not affect them. Thus, the transformations applied by pgfpages to put the pages where you want them are (cannot, even) be applied to the coordinates of hyperlinks. It is unlikely that this will change in the foreseeable future.

That's imho why links works more or less ok on the main slide when you put the notes on the right (it does for me when I compile with a current texlive live, including the outlines): As pgfpages inserts the notes into the main slide on the right the absolutes coordinate are not changed. If you put the notes on the left and hover with your mouse around the notes you will see that the links are there.

With handouts with 2 on 1 layout there is imho no chance to get working links. Here both pages are reinserted in a third and this looses anotations anyway (in addition to the coordinate problem which would exist here too).

Answer 2

I cannot post a comment, but if the pgfpages package is the problem you could use PDFjam in the shell.