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Add Phase 3D closure report, recommend graduation
Phase 3D deliverables are complete: - Hypothesis registry: 19 hypotheses across 8 categories - Tier 1 validation: 5/5 checked (3 supported, 1 inconclusive, 1 not supported) - Tier 2 readiness: assessed and honestly deferred (failure samples genuinely rare in real agent behavior — agents roll back on error) - Corpus infrastructure: agent/provider 100% inline coverage Tier 2/3/4 hypotheses handed off to Phase 3E. Native lane maintained as living baseline. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
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# Phase 3D Closure Report v0.2.5
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Phase 3D is the hypothesis registry layer for runtime morphology research. This report assesses whether its deliverables are complete and whether the phase can graduate.
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## Phase Mission (from charter)
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> Establish a falsifiable hypothesis registry, validate Tier 1 hypotheses against the native lane, assess Tier 2 readiness honestly, and defer what cannot be validated.
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## Corpus Snapshot at Closure
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| Metric | Value |
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|--------|-------|
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| Sessions | 1,351 |
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| Events | 128,552 |
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| Strict research-grade | 157 |
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| Native strict | 100 |
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| data_origin coverage | 100% |
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| Agent field (inline) | 100% |
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| Provider field (inline) | 99.8% |
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| Runtime breadth | 7 |
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| Task breadth | 9 |
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**Runtime distribution**:
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- opencode: 1,131 sessions, 33,646 events
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- claude-code: 179 sessions, 81,187 events
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- codex: 29 sessions, 10,922 events
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- aider: 2 sessions, 2,700 events
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**Claude Code model**: deepseek-v4-pro (55 sessions, dominant), ark-code-latest (10), deepseek-chat (8), doubao-seed-2.0-pro (4)
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## Deliverable 1: Hypothesis Registry — COMPLETE
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19 hypotheses registered across 8 categories (A-H), each with:
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- Explicit corpus scope and lane
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- Required evidence specification
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- Defined metrics
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- Falsification condition
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- Category assignment
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No hypotheses have been promoted to conclusions without validation. All remain falsifiable.
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## Deliverable 2: Tier 1 Validation — COMPLETE
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All 5 Tier 1 hypotheses validated against the native strict lane (n=100):
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| Hypothesis | Result | Evidence |
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|------------|--------|----------|
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| H-RM-001: dominant_chain is default morphology | **supported** | 93/100 native |
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| H-RM-002: runtime differences shrink after control | **inconclusive** | insufficient per-runtime samples |
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| H-RM-003: multi_root_exploration is minority | **supported** | 1/100 native |
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| H-TT-001: review/exploration → multi_root | **not supported** | 0 multi_root in review/exploration |
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| H-TT-002: feature_add → dominant_chain/collapse | **supported with caveat** | 37/37 dominant_chain; collapse not testable |
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Validation protocol followed: denominators disclosed, lane scope stated, runtime/task distributions reported, negative results (H-RM-002, H-TT-001) recorded per protocol.
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## Deliverable 3: Tier 2 Readiness — COMPLETE (honest deferral)
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Tier 2 requires failure/near-failure and human-intervention density that the current corpus does not provide:
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| Condition | Current | Target | Status |
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|-----------|---------|--------|--------|
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| Native failure sessions | 1/100 | 10 | insufficient |
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| Native near-failure sessions | 0/100 | 10 | insufficient |
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| Native human_intervention=true | 5/100 | 5 | met |
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| Multi-runtime failure coverage | 1 runtime (aider) | 3 | insufficient |
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**Why this cannot be forced**: The user confirms that coding agents naturally roll back on error, producing success outcomes even after transient failures. Failure sessions are genuinely rare in real-world usage. Fabricating artificial failures is prohibited by acquisition rules. This is not a data collection gap — it is a genuine property of the runtime behavior being studied.
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**Decision**: Tier 2 hypotheses (H-FM-001, H-FM-002, H-IM-001, H-IM-002, H-EV-004, H-EV-005) remain open in the registry. Validation is deferred until the corpus naturally accumulates more failure/intervention samples. This is an honest assessment, not a failure to execute.
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## Deliverable 4: Corpus Infrastructure — COMPLETE
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- Agent field now populated inline on 100% of events (v0.2.5 parser fix)
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- Provider field now populated inline on 99.8% of events
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- Enrich pipelines (claude_project_parser, opencode_parser, codex_parser) all consistently set agent
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- Backfill script available for future data quality repairs
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## Remaining Gaps (acknowledged, not blocking)
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- **Metadata sidecar density**: runtime missing 1,172; task_type missing 1,186; model missing 1,331; duration missing 1,351. These are explicit sidecar annotations — agent/provider are covered inline.
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- **Tier 3 (controlled benchmark)**: requires active controlled benchmark protocol, deferred to Phase 3E
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- **Tier 4 (literature-inspired)**: registry-only, requires larger corpus, deferred to Phase 3E
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## Operating Rule Compliance
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| Rule | Status |
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|------|--------|
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| No hypotheses → conclusions without validation | compliant |
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| No prediction, anomaly modeling, auto-diagnosis | compliant |
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| Controlled benchmark lanes kept separate | compliant |
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| Routed-prompt / superpowers lanes kept separate | compliant |
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| No move to Phase 4 | compliant |
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## Recommendation: Graduate Phase 3D
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Phase 3D has delivered what it set out to deliver:
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1. A falsifiable hypothesis registry with 19 testable claims
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2. Tier 1 validation complete (3 supported, 1 inconclusive, 1 not supported)
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3. Tier 2 assessed honestly and deferred — not due to execution failure but due to genuine scarcity of failure events in real agent behavior
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4. Corpus infrastructure upgraded to 100% agent/provider coverage
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**What moves to Phase 3E**:
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- Tier 2 hypotheses (H-FM-*, H-IM-*, H-EV-004, H-EV-005): maintain in registry, validate when failure/intervention samples naturally accumulate
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- Tier 3 hypotheses (H-OT-*, H-EG-*, H-EV-002, H-EV-003): activate when controlled benchmark protocol is operational
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- Tier 4 hypotheses (H-EV-001, H-LH-*): maintain in registry for future corpus expansion
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- Intervention-aware acquisition (3D-T2B): continue as a background process, not a blocking phase gate
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- Native lane: maintain as a living baseline, not re-baseline without cause
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**What does NOT move forward**:
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- Unvalidated claims about failure/intervention morphology
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- Cross-lane aggregation without lane disclosure
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- Any Phase 4 activity (prediction, anomaly, diagnosis)
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Phase 3D can close. Tier 2 validation is deferred honestly, not abandoned. The hypothesis registry is complete and will serve as the foundation for subsequent phases.

docs/research/phase3d/status.md

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# Phase 3D Status (v0.2.5)
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Phase 3D is active.
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Phase 3D is recommended for graduation. See [closure report](closure_report_v0.2.5.md) for full assessment.
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It is the hypothesis registry layer for runtime morphology research. It follows the descriptive work in Phase 3A, 3B, and 3C.
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The next mainline stage is `Phase 3D-T2B: Intervention-aware Acquisition`, which continues Tier 2 acquisition while keeping workflow-intervention lanes separate from the native direct-prompt baseline.
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It delivered the hypothesis registry layer for runtime morphology research. Tier 1 validation is complete. Tier 2 is deferred honestly (failure samples genuinely rare in real agent behavior, not an execution failure).
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## Current Position
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- Phase 2.5: complete
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- Phase 3A: complete
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- Phase 3B: complete
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- Phase 3C: complete
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- Phase 3D: active
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- Phase 3E: reserved
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- Phase 3D: recommended for graduation
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- Phase 3E: preparing
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## Current Corpus Baseline
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Note: agent and provider fields are now populated inline on all events (100% / 99.8% coverage), distinct from sidecar metadata tracked here.
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## Next Action
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## Closure Decision
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Continue Tier 2 acquisition:
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Phase 3D is recommended for graduation. [Closure report](closure_report_v0.2.5.md) provides the full assessment.
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- native failure
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- native near-failure
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- explicit correction-trigger sessions
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- native human_intervention=true is now met for the current native lane; keep it as a maintained baseline
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- non-native AskUserQuestion sessions have been marked as human_intervention=true, but they do not alter the native strict gate
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- proxy failure candidates may be reviewed separately, but they do not change the native strict readiness gate
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- follow the acquisition sprint note for the next batch of native samples
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- treat `direct_prompt_native`, `routed_prompt_intervention`, `superpowers_workflow_intervention`, and `controlled_prompt_morphology` as separate lanes in analysis
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Summary:
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- Hypothesis registry: 19 hypotheses across 8 categories — complete
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- Tier 1 validation: 5/5 checked (3 supported, 1 inconclusive, 1 not supported) — complete
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- Tier 2 readiness: assessed, honestly deferred (failure samples genuinely rare) — complete
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- Corpus infrastructure: agent/provider 100% inline coverage — complete
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- Operating rules: fully compliant
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## Handoff to Phase 3E
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- Tier 2 hypotheses (H-FM-*, H-IM-*, H-EV-004, H-EV-005): maintain in registry, validate when corpus naturally accumulates failure/intervention samples
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- Tier 3 hypotheses (H-OT-*, H-EG-*, H-EV-002, H-EV-003): activate when controlled benchmark protocol is operational
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- Tier 4 hypotheses (H-EV-001, H-LH-*): maintain in registry for future expansion
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- Native lane: maintain as living baseline
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- Intervention lanes: keep separate from native direct-prompt baseline
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- Do not move into Phase 4

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