Add `listDtdUris` command to the DTD tool, drop auto DTD connection logic. (#418)

Related to https://github.com/dart-lang/ai/issues/416.

This changes the flow for connecting to DTD to require an extra tool call in most cases (list then connect), but also makes things a lot more explicit and also less confusing for the agents.

Eventually, this `listDtdUris` command should become just a skill or something like that, but given it is a new command agents won't know about it out of the box, and adding it as an MCP subcommand should make things much more reliable in general.

Also adds the application name if provided when listing apps, and fixes a bug where _all_ connected apps would be listed under each DTD URI, instead of only the apps relevant to that DTD instance.