Fix cfgupgrade with non-default DATA_DIR

Commit 43575108 added bootstrap.GenerateclusterCrypto and commit
7506a7f1 changed cfgupgrade to use it. However, this lost the
functionality of upgrading in non-default DATA_DIR.

To fix this, we enhance bootstrap.GenerateclusterCrypto to accept custom
file paths for the three files it modifies. If more files will be needed
in the future, we could just pass in modified DATA_DIR, but for now it
suffices.

Signed-off-by: Iustin Pop <iustin@google.com>
Reviewed-by: René Nussbaumer <rn@google.com>