chore(absence): serialization hardening, renderer DRY, hygiene

[HumanBean17]

Applies the deferred follow-up backlog from the absence-diagnosis review. No change to the diagnosis logic itself — full suite green (1261 passed).

Changes

absence_vocab.py — serialization hardening

• FORMAT_VERSION constant + load() validation: a sidecar with an unknown/changed JSON shape now raises VocabIndexStale (→ rebuild) instead of being misread. format_version was written but never checked.
• Atomic save(): dump to a temp sibling + os.replace, so a crash mid-write leaves the previous complete file or the new one — never a truncated sidecar. Explicit utf-8 / ensure_ascii=False.
• Drop _name_index from the sidecar: derivable from records, rebuilt in __init__ on load (single source of truth, no bloat). Backward-compatible — old sidecars with name_index load fine (field ignored).
• Collapse the redundant except (VocabIndexStale, FileNotFoundError, Exception) tuple (Exception subsumes the others).

jrag_render.py — DRY + message rendering

• Extract _ABSENCE_VERDICT_TEXT + _verdict_line() — the verdict→label mapping was triplicated across not-found / listing / traversal empty.
• Render absence.message in the not-found block (the authored per-cause help was being dropped on the CLI surface).
• Remove unreachable else branches (verdict is a closed Literal).

absence_diagnosis.py — correct the _threshold_verdict docstring (only absence_absent_floor decides; close_threshold is transparency-only here, decides the find path).

Hygiene — stop tracking the generated vocab_index.json (+ its atomic-write .tmp); it dirtied every tree on a test/build run via a regenerated built_at. Rebuilt on demand.

Deliberately NOT done (would not improve correctness)

• Live-graph version compare: comparing the sidecar to the live graph's ontology version (instead of the code constant) would weaken staleness detection — it could accept an index built under an older ontology. The code-constant compare is the safer, correct choice for schema incompatibility.
• SymbolRecord.resolved default: leaving it required is safer (explicit > implicit); _row_to_symbol_record already defaults missing→True.

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