Disable shallow clone by default except for opam repositories

[kit-ty-kate]

Fixes #6145
Backported to the 2.2 branch by #6147

[reynir]

To clarify the opam repository pulls/clones are shallow due to this this constant value and not relying on the defaults of the optional argument:

opam/src/repository/opamVCS.ml

Line 45 in 6effccc

let full_fetch = false in

[rjbou]

linked to #5888 (comment)

[rjbou]

lgtm, thanks!
I've added a test for fetching a package that highlights the behavior change on several cases. For repo fetching, as there is no change, it ensures that the repository is still fetched with no history.