[hiracchi]

Summary

• File → "Open Plot (pytools)..." (renamed from "Open Plot (pytools JSON)...") now reads a pdf-plot/1 plot written as YAML (.yaml, .yml). The data model is unchanged, so a file can be written or edited by hand (comments, no commas).
• JSON (.json) is still read, only as a transitional measure until ProteinDF_pytools writes YAML; it will be removed then. (The YAML reader accepts JSON, so no second parser is kept; serde_json is dropped from core.)
• Elements are read as text, so an element named No stays an element (tested).
• architecture / ROADMAP / CHANGELOG (EN/JA) updated.

Checks (scripts/check.sh --trunk)

All 8 PASS.

Not checked

• A file written by ProteinDF_pytools (it writes only --json so far; a request for YAML output is the next step).
• Clicking in a real window with a loaded structure (same limit as the other plot PRs).