docs(sync): register the Protobuf importer everywhere importers are listed

#128 only updated SKILL.md, the toolbox section and the cookbook:

- README.md / README_CN.md: the extractor count and list (13 -> 14), the
  Schemas-and-pipelines highlight, and the jgraph-plugin comparison.
- references/diagram-ir.md: the `build --from auto` source list.
- references/mcp.md and scripts/diagramctl_mcp.py: the MCP `build`
  description and its `source_type` enum.
- references/toolbox.md: the focused-tool count (39 -> 40).

CHANGELOG: the feature bullet moves from the released [3.2.4] section to
[Unreleased]; the version bump happens in the release commit.