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Rectifies all gaps from the 2026-08-22 onboarding assessment. Phase 0 — data model: - Add ExecutionResult.lsp_enabled / plugins_loaded / mcp_loaded fields. - MetricCollector.infer_tier now uses the explicit field (not bool(diagnostics)). Phase 1 — LSP feedback loop: - New evaluation/lsp_feedback.py with wrap_prompt_for_lsp() and run_lsp_iteration_loop() (max 3 rounds). Phase 2 — AblationRunner: - New evaluation/ablation_runner.py drives 5 explicit tier cells via BenchmarkRunner._run_cell; --ablation CLI flag; full Markdown proof matrix renders at the end of the run. Phase 3 — Agent engine integration: - Move scripts/agent_engine.py -> agents/agent_engine.py (importable). - New agents/agent_engine_adapter.py registered as 'agent-engine'. - BaseAgentAdapter._should_fallback_to_engine + _execute_with_engine_fallback guarded by HARNESS_BENCH_FALLBACK_ENGINE=1. Phase 4 — Bubblewrap sandbox: - BaseAgentAdapter._wrap_with_bwrap() opt-in via HARNESS_BENCH_USE_BWRAP=1. Falls back to plain cmd when bwrap is missing. Phase 5 — Cleanup & docs: - Delete reporting/junit.py; rewire tests/test_core_and_reporting.py to use the canonical metrics/junit_exporter.py. - README: ## Prerequisites section + illustrative banners above the empirical tables + reproduction recipe. - CLAUDE.md / AGENTS.md: match the new env toggles table + prerequisites. - scripts/install_harness.sh: copy agent_engine.py from agents/ (not scripts/). Phase 6 — verification: - 86 tests pass (up from 55). ruff check + format clean. - Smoke + ablation + bwrap + fallback integration paths verified locally. Co-Authored-By: Claude <[email protected]>