Download bundle manifest as bundle.json

[diekhans]

hca dss download and hca dss download-manifest do not include bundle.json
files in the download. The bundle.json contains information not available in any of the downloaded metadata files and is key to understanding the bundle.

[hannes-ucsc]

To clarify, bundle.json is an arbitrary name that bears no significance in the metadata or the DSS. The DSS refers to this JSON structure as the bundle manifest. It is the object that represents a bundle in the DSS and that makes up the response of GET /bundles/$uuid.

It does make sense to store the bundle manifest in a file called bundle.json on the user's disk. To fit into the .hca cache implemented in #234, the primary location of this file should be .hca/bundles/$bundle_fqid with a user-friendly hardlink in $bundle_fqid/bundle.json