Add manifests to assembled binary JARs

[DanielThomas]

Binary JARs assembled by ja currently suppress the default manifest, which makes java -jar report them as invalid or corrupt when they do not provide one.

• allow jar to generate its default manifest for binary artifacts
• pass source-provided manifests through --manifest so their attributes are retained
• retain the existing no-manifest behavior for source and Javadoc artifacts
• cover default manifests, source attributes, and synthesized Main-Class values

Testing

• ja test --all (387 tests passed)