Manifest (13): update for recent changes

This is a small subset of !3366 (merged), which aims at generating dune and .opam files from a manifest.ml file. See !3366 (merged) for a broad view of the end goal.

The goal of this MR is to keep the diff of !3366 (merged) small by merging the generated version of dune and .opam files without waiting for !3366 (merged). This means mostly whitespace changes, but there can also be fixes to dependencies.

General Review Tips

I left comments in the MR to explain some of the changes. I suggest you read them first.

patdiff helps a lot, as well as the -w option of git diff. You can use patdiff with git diff as follows:

opam install patdiff
export GIT_EXTERNAL_DIFF=`pwd`/_opam/bin/patdiff-git-wrapper

If you read the diff in GitLab, the -w option of git diff can be activated by opening preferences (the gear icon while reviewing) and unchecking "show whitespace changes".

Apparently, VS Code is also very nice to review whitespace diffs.

Manually testing the MR

Compile everything (or let the CI do it for you).

Checklist

• Select suitable reviewers using the Reviewers field below.
• Select as Assignee the next person who should take action on that MR