Re-add alignment vignette

[jorainer]

This re-adds the alignment vignette. At present, the RData result object is build by running the end-to-end qmd while docker image creation, copying that file then to a (publicly accessible) folder within the docker image. This workaround was needed, because it seems that it's not possible to save data outside the working directory in which quarto runs. Also, the GHA that runs pkgdown does not use /home/rstudio as working directory, and hence the RData (if saved within e.g. /home/rstudio/vignettes) can not be found.

Another workaround that was needed to enable pkgdown with quarto was to change the location of the R temporary directory and set it to a folder that is in the same shared folder as the working directory the GHA uses (i.e. under __w/).

We should/could think of a cleaner solution, but this works for now.

[philouail]

Thanks ! for sure I will check on my side also how to fix this. I think later we will not be saving the Rdata object anyway so let's see.