Allow manifest to have default/clone-depth

[galak]

Allow to set clone-depth as a default in the manifest. A clone-depth set on a specific project should override the default.

[mbolivar-nordic]

I'm going to close this as not planned because over time, we've added options like --fetch-opt, which address the use case of needing to make shallow clones in CI environments. I believe this use case is what was originally motivating this issue. Please reopen and explain the use case if that's wrong.