v0.6.0: Proactive provenance (run-record + node runner) + LaTeX paper standard

[hebbianloop]

Summary

Makes the Glimmer graph executable, not just descriptive, and establishes a LaTeX standard for submittable papers.

The agentic loop (docs/agentic-loop.md) was specified but had no runtime primitive; the only "verification" script re-hashed files on disk ("not a full re-run"). This PR closes that gap with one core node type and one tool, and lands two manuscripts.

Schema (v0.5.1 → v0.6.0)

• run-record core node type — one concrete, replayable invocation (PROV Activity) with a planned → ready → running → executed lifecycle, binding a method + pinned, standard-validated inputs + expected outputs + command + container digest + a runner-written verdict. The executable unit of the agentic loop.
• New edges reruns / consumes / regenerates / emits (+ inverse regenerated-by); tests-hypothesis / addresses-concept allowed from a run-record.
• Method-registry affordances: registry-ref + implements / equivalent-to / refines. standard.validator hint for the runtime gate.

Runner — glimmer/tools/run.py (glimmer run / glimmer rerun)

• Pre-run standards gate (inputs pinned AND valid; delegated to each standard's validator).
• datalad containers-run replay (feature-detected; degrades honestly).
• Three verification tiers: byte-identical (NIfTI/GIFTI/JSON normalization), numeric-within-tolerance (re-derive published numbers), structural (agent/LLM).
• certify_equivalence, dependency-ordered all, provenance manifest, verdict writeback.

Validator, example, docs

• validate.py: run-record field/edge/target/lifecycle checks + agent-protocol rule.
• examples/synthetic-provenance/: exercises the loop + all three tiers + the gate + equivalence, no real data / no heavy deps.
• New docs/proactive-provenance.md; agentic-loop.md made executable; roadmap renumbered (federation → v0.7, registry/minimal-path folded in); README repositioned as AI-native reproducibility; agent-protocol + datalad-pattern cross-linked.

Papers (new LaTeX standard)

• papers/glimmer-paper.cls — venue-neutral house class; papers/README.md documents the convention.
• Paper 1 (01-knowledge-graph-navigation/) — scoped to v0.5: the graph as a navigable substrate; verification as a validator-enforced contract, the executable runner named as forthcoming. Preprint candidate (9pp).
• Paper 2 (02-proactive-provenance/) — v0.6: the run-record + node runner (7pp). LaTeX port of docs/paper-draft.md.

Verification

• glimmer validate on the synthetic example: 0 errors. glimmer rerun … all → 100% (verified ×2, reproduced-within-tolerance, structurally-valid).
• Negative controls: gate-fail (exit 1), tamper → mismatch, offline → inputs-unavailable, equivalence certified by output-match.
• Backward-compat: ds000114-nipype validates unchanged.
• Both papers compile via make (latexmk + bibtex), no undefined references.

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