How can I output the appendix in a separate pdf

For conferences (such as ICML) you sometimes have to submit the appendix as a separate pdf.

In the Appendix I want to use packages such as hypperref/cleveref to reference to equations and theorems from the main paper and I want all counters continue counting from where I stopped in the main part: If there is already an equation (1) in the main part, there shouldn’t be any equation (1) in the appendix (otherwise referencing to eq.~(1) can lead to misunderstandings).

I also want the solution to be compatible with bibtex. What is the best way to get this result?
I would imagine somewthing like setting a variable at the beginning of the document if eighter only the main paper, or only the appendix or both are put into the resutling pdf.

Is there a standard solution for this?