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Catchup 13: Merge agent wave1 step#47

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jmsexton03 merged 186 commits into
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catchup_13_merge_agent_wave1_step
Mar 26, 2026
Merged

Catchup 13: Merge agent wave1 step#47
jmsexton03 merged 186 commits into
developmentfrom
catchup_13_merge_agent_wave1_step

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Summary

  • Catchup context: slice 13 on branch catchup_13_merge_agent_wave1_step.
  • Ordered split wave objective: preserve parity/paper cutoff lineage by landing slices in ascending order.
  • What was added/changed in this slice:
    • merge wave1-wt-4 and stabilize step-1 unit suite
    • add new unnumbered regression tests for metrics, routing, and monitoring
    • updated stabilize unit contracts and restore legacy compatibility paths
    • updated fix unit-test collection imports for knowledge and architect services
    • updated fix benchmark seed=0 handling and replay manifest privacy
    • updated architect retrieval/orchestration updates and sweep normalization
    • updated schema builder non-blocking tier logging and config safeguards
    • updated mCP session context persistence and server concurrency guardrails
  • Workstreams (topic-level):
    • index/schema artifact and metadata evolution
    • MCP boundary and payload-handling updates
    • runtime graph routing/wiring updates
    • graph/model state-contract updates
    • service contract/behavior updates
    • unit regression coverage updates
    • clarification flow behavior adjustments
    • sweep/orchestration behavior adjustments
    • MCP safety/contract handling adjustments
    • FAISS/manifest compatibility handling
  • Slice metadata:
    • Commit range: f4206ae0fcbd..523aba32ad20 (source apply_stack_slice_113 -> canonical fix_stack_main)
    • Findings profile (P0/P1/P2/P3): 3/0/2/0 (total 5)
  • Fix implementation note: findings are reconciled/resolved on canonical stacked branch fix_stack_main at 73f37cf9e86d.

Related or overlapping functionality / DRY guidance

  • Overlap is expected with stacked fix lineage (fix_stack_main); avoid duplicating logic that is already hardened in shared services/nodes.
  • Keep node/state contract compatibility aligned with src/models/graph_state_canonical.py and tests/contracts/* when touching shared flows.
  • Evidence artifacts for cross-slice decisions: artifacts/integration/findings_reconciliation.json and artifacts/integration/fix_branch_remap_impact.md.
  • This embeds a significant architectural decision that needs an ADR.
    • If checked, add an ADR under docs/adr/ (one short file describing context, decision, consequences).

Impact checklist

  • fixes a bug or incorrect behavior
  • adds new capabilities
  • changes answers in the test suite to more than roundoff level
  • likely affects downstream users or results
  • includes docs updates (code/docs), if appropriate
  • none of the above

Tests run (CI runs: pytest tests/unit, pytest tests/quality, pytest tests/integration -m "integration_l1 or integration_l2 or integration_l3 or integration_l4 or integration_full")

  • tests/unit: pytest tests/unit
  • tests/quality: pytest tests/quality
  • integration ladder (CI): pytest tests/integration -m "integration_l1 or integration_l2 or integration_l3 or integration_l4 or integration_full"
  • other (list): final closure validation on canonical fix_stack_main
  • Output/summary:
    • per-slice branch-head run in this phase: not executed
    • canonical closure branch used for validation: fix_stack_main (73f37cf9e86d)
    • canonical unit: 1663 passed, 31 skipped, 3 warnings (coverage 56.82%)
    • canonical full: 1813 passed, 78 skipped, 10 xfailed, 11 warnings (coverage 58.63%)
    • canonical quality: 20 passed, 1 skipped, 5 warnings
    • canonical integration ladder: 47 passed, 36 skipped, 92 deselected, 1 xfailed, 7 warnings
    • canonical junit evidence: artifacts/integration/reports/fix_stack_main_20260318_034847/unit.junit.xml, artifacts/integration/reports/fix_stack_main_20260318_034847/full.junit.xml
  • If tests require repos/schemas/indices or real services, note markers used.
  • requires_solver(...) implies repo + schema + default indices are available locally.
  • Use -k pelec|erf|amrex|warpx to filter solver-specific tests.

Tests not run in CI (required if any)

  • CI runs tests/unit, tests/quality, and tests/integration with integration_l1..l4 + integration_full markers via micromamba; list anything else not covered by CI here.
  • None
  • tests/e2e
  • other (list): per-slice branch-local test reruns
  • Reason for skip: this phase validated closure on canonical stacked branch (fix_stack_main) rather than re-running each catchup branch independently.
  • Risk/mitigation: parity/open-PR coverage gate rerun is explicitly queued in the handoff for network-enabled execution.

Notes (optional)

  • Manual output / logs (short):
    • Validation bundle: artifacts/integration/reports/fix_stack_main_20260318_034847
    • Reconciliation totals: total_findings=109, addressed=109
    • Remap artifact: artifacts/integration/fix_branch_remap_impact.md
  • Known limitations:
    • Catchup PRs are split for ordering/parity traceability; final integrated evidence remains anchored on fix_stack_main artifacts.

Labels (optional)

  • Not applicable for these ordered catchup PRs; label hygiene is deferred to maintainer-side triage.

- Enhances aggregate-metrics extraction for model/provider and strategy fields.

- Adds grouped summary outputs and publication table generation paths.

- Covers CLI/report outputs for directory and file input workflows.
- Hardens MCP session context merge/persist behavior with parent inheritance.
- Adds server-side concurrent session handling safeguards.
- Verifies workflow-store and MCP concurrency behavior end-to-end in tests.
- Adds non-blocking Tier 3/4 logging behavior to schema build workflow.

- Improves config/schema integration guardrails for edge-case handling.

- Covers builder/config boundary behavior with dedicated unit tests.
- Refines architect retrieval and solver-selection orchestration behavior.
- Updates knowledge-service normalization and related orchestration tests.
- Keeps sweep/orchestrator test expectations aligned with service behavior.
# Conflicts:
#	scripts/aggregate_metrics.py
#	src/config.py
#	src/graph.py
#	src/nodes/paper_validator_node.py
#	src/services/architect.py
#	src/services/plan.py
#	src/services/rules/base.py
#	src/session_manager.py
#	src/utils/metrics.py
#	tests/quality/test_standards.py
#	tests/unit/test_architect_node_history.py
#	tests/unit/test_benchmark_runner.py
#	tests/unit/test_level0_index.py
#	tests/unit/test_metrics_collector.py
Comment on lines +25 to +35
MAX_NEW_INTEGRATION_LOC = 300
LEGACY_LOC_BUDGET_EXEMPT_CODES = {
"AMReX",
"PeleC",
"PeleLMeX",
"Incflo",
"WarpX",
"ERF",
"REMORA",
}

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too specific, maybe this doesn't live here

@jmsexton03 jmsexton03 left a comment

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Needs cleaner test names

@jmsexton03 jmsexton03 marked this pull request as ready for review March 26, 2026 16:12
@jmsexton03 jmsexton03 merged commit 05a5a18 into development Mar 26, 2026
11 of 15 checks passed
@jmsexton03 jmsexton03 deleted the catchup_13_merge_agent_wave1_step branch March 31, 2026 17:17
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