Refine exit code for shed_update

I believe `shed_update` returns a non-zero exit code if `--check_diff` detects no difference even if the shed metadata has been modified. Currently planemo doesn't even check if the metadata is different - it always just does a PUT and doesn't inspect the results. I think the whole thing should be refined to deal with these limitations.

Start by tracing the shed_update command and its --check_diff handling, then inspect where the PUT request is made and how its result is used. Clarify the expected exit code when metadata changes without a code difference, and define completion by checking both metadata differences and the update response.

Written by the indexing model from the issue text.