pdb2reaction

Changed

• Docs restructured for newcomer onboarding (EN+JA): goal-based 4-card "Start here" map on docs/index.md; unified 5-bullet "At a glance" block on all 11 calculation command pages; unified Quickstart template; getting-started.md workflow-modes table + flag matrix trimmed; installation.md split into Required vs Optional with the MACE+UMA conflict promoted to a {warning}; dft.md size/OOM caveats consolidated into a single "Practical limits" subsection.
• Reference duplication eliminated — each canonical fact has exactly one home and is cross-linked from every other page: --selected-resn ID-vs-name (cli-conventions.md (selected-resn-takes-ids)), --opt-mode polysemy ((opt-mode-semantics)), --engine / --dft-engine alias ((engine-vs-dft-engine)), exit-codes table ((exit-codes)), 5 cm⁻¹ vs 100 cm⁻¹ TS thresholds (glossary.md (imaginary-mode-thresholds)), scan-list spec ((scan-list-spec)).
• Command pages (tsopt, path-search, path-opt, opt, freq, irc) no longer reproduce the YAML schema; canonical schema lives in yaml-reference.md. ~1500 lines of duplication removed; only command-specific overrides remain inline.
• recipes-common-errors.md is now a symptom→page router; detailed fixes live in troubleshooting.md.

Added

• glossary.md (EN+JA): DFT//MLIP entry.
• yaml-reference.md overview: rsirfo "Used by" lists tsopt, all (was tsopt).
• getting-started.md "Important CLI options": --opt-mode-post grad|hess (all-only).

Fixed

• docs/ja/extract.md: typo :electric → :charge.
• docs/ja/cli-conventions.md --selected-resn: previously claimed silent no-match; corrected to match the actual ValueError raised when residue-name tokens are passed.
• docs/yaml-reference.md IRC: removed redundant calc.return_partial_hessian bullet duplicating the preceding line (EN+JA).
• docs/ja/getting-started.md: corrected relative path to reference/commands/index.md.