change default output format for most commands to .sig.zip

[ctb]

The discussion around lazy loading, manifests, and so on is converging, for me, on recommending .zip files and standalone manifests as being the Right Set of Output Files for lazy loading - see #1895.

I think .sig.zip is much better than sig.gz because it supports lazy loading; and just .zip might be confusing.

Related issues:

• change sourmash sketch to output .sig.gz by default #1876
• sourmash sig split should output .zip or .sig.gz files by default #2703