Don't override the whole step when updating valohai.yaml with vh step command

[noorula]

Currently, if you run the vh yaml step <filename> command, it will override the previous step yaml definition. If the user has defined some properties, e.g. no-output-timeout, by hand, they will be overridden. This is somewhat inconvenient as this might easily go unnoticed by the user.

It would be great if the command only updated the properties defined in the valohai.prepare() and didn't touch the other ones.