When a user provided the `--ca-file` flag to the `bootstrap` command,
the given CA file wasn't taken into account for cloning the repository
locally. It was just passed along to the CR that is created so Flux
can make use of it when cloning the repository in-cluster.

However, users may not want to add a custom CA to their local host's
trust chain and may expect the `--ca-file` flag to be respected also
for cloning the repository locally. This is what this commit
accomplishes.

closes #1775

Signed-off-by: Max Jonas Werner <mail@makk.es>