Proto manager: add copy for stabilise

What

This MR reworks some modules of proto_manager and then adds the command copy that is a part of proto_manager stabilise.

This MR limits overlapped modifications between commits in the cost of the code compilation fails between some commits of this MR.

Why

How

Manually testing the MR

To check that proto_manager is equivalent to proto_manager.sh, the script git_diff_commits.sh (author @MBourgoin) will be used. This script does the diff between diffs of 2 branches.

1. Create the reference branch using proto_manager.sh

⚠️ proto_manager.sh may fail, but until it generates at least the 10 first commits, it permits to test this MR.

git checkout -b proto-manager_ref master
git pull --rebase origin master
make
./scripts/proto_manager.sh --stabilise -f alpha -t beta
git log
ref_start= #put the commit hash of "Beta/src: copy from alpha"
ref_end= #put the commit hash of "Beta/manifest: make manifest"

2. Runs the proto_manager

git checkout vivien@proto-manager_copy
git pull --rebase origin master
make
dune exec devtools/proto_manager/main.exe -- stabilise -f alpha -t beta
git log
test_start= #put the commit hash of "Beta/src: copy from alpha"
test_end= #put the commit hash of "Beta/manifest: make manifest"

3. Do the diff between ref and MR branch diffs

wget https://gitlab.com/-/project/3836952/uploads/91e3cce1c92d29b2dc1a0904300ceedb/git_diff_commits.sh
chmod +x git_diff_commits.sh
./git_diff_commits.sh $ref_start..$ref_end $test_start..$test_end

You should observe differences only on the commit hashes and the dates.

Checklist

• Document the interface of any function added or modified (see the coding guidelines)
• Document any change to the user interface, including configuration parameters (see node configuration)
• Provide automatic testing (see the testing guide).
• For new features and bug fixes, add an item in the appropriate changelog (docs/protocols/alpha.rst for the protocol and the environment, CHANGES.rst at the root of the repository for everything else).
• Select suitable reviewers using the Reviewers field below.
• Select as Assignee the next person who should take action on that MR