also disable shallow clone when retrieving manifest "from-git" with --from-git

[ph1l]

When doing an initial clone of a repo to get the manifest from a git repo hosted by a HTTP (or HTTPS) server, shallow clones fail with the following message:

Initialized empty Git repository in /home/purism/.flatpak-builder/git/https_domain.com_code_repo.git-L04WW1/
Fetching git repo https://domain.com/code/repo.git, ref refs/heads/phil/flatpak
fatal: dumb http transport does not support shallow capabilities
Can't clone manifest repo: Child process exited with code 128

adding the --no-shallow-clone doesn't change the behavior for this --from-git= clone. This patch fixes the behavior and makes it work as exepected for me.

fixes #501