Zed collab-staging: acp_thread: Apply v2 metadata patches by key (#65709)

• Delegate v2 entity _meta patches to the SDK helper for
  user/agent/thought messages, tool calls and permission subjects,
  terminal display state, session info, and compaction.
• Preserve omitted keys, remove keys set to null, replace nested values
  whole, retain nested null data, and honor whole-field null clears. Empty
  objects and removals of absent keys have no effective-change signal.
  Explicit clears also clear derived tool hints.
• Keep wire provenance through session-info updates and the list
  notification lane rather than erasing it in a v1-to-v2 conversion. V1
  session-info omission/null behavior and full metadata replacement remain
  unchanged; v1 compaction retains its own omitted/null/replacement rules.
• Preserve snapshot metadata literally. In particular, v2 list entries
  no longer route their metadata through an upsert; null-valued keys
  remain data. Content/chunk, terminal output/exit snapshot, and plan
  metadata stay separate from entity metadata.

Release Notes:

• N/A