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Implements docs/done/work-graph-node-execution-deblackbox-requirements.md end to end. The three documented call sites (e2e_pipeline.py:: _check_prd_consistency, work_graph_orchestrate.py::_llm_judgment_verify_fn, work_graph_orchestrate.py::_make_run_fn) all used to render a one-off Dynamic Workflow .js script and run it via `claude -p 'Run /<name>...'` purely to get "agent identity + schema-shaped output" -- a workaround for --json-schema silently conflicting with --agent (05 §5.4.1.1). That workaround was never actually necessary: work_graph_plan.py:: plan_work_graph() solved the identical problem from day one with a flat `claude --agent ... -p ...` call + ```json-fence extraction from free text, already validated in production. New org_node_trigger.trigger_org_node_structured() unifies all three call sites onto that same flat-call approach. extract_json_payload() generalizes work_graph_plan.py's fence-extraction algorithm; _extract_graph_manifest is now a thin wrapper over it. Two more call sites not in the original design doc (written before they existed) were found and migrated too: _run_reflection_perspective and _fix_skill_for_node (Phase 2a's Reflection-review/Fix-Skill). work_graph_fork.py needed no changes -- it only reaches _make_run_fn indirectly via run_graph(), so it benefits automatically. FR-4's real-agent verification (RUN_REAL_AGENT_E2E=1, mandatory, not optional -- src/test_org_node_trigger_e2e.py) confirmed persona loading, --model override, and JSON-fence extraction all work against a real model. write_workflow_script/execute_work_graph/execute_work_graph_with_usage_ limit_retry are confirmed to have no remaining production callers; docstrings mark them historical, the file is kept (not deleted). Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Per CLAUDE.md's docs/ role split (todo = pending, done = shipped into the SDD/code): all seven Graph Engineering series items with a real implementation (B, D, E, F, G, H -- A had no separate doc, resolved directly in graphlemon_architecture.md; C is explicitly won't-do) now have their requirements+design docs moved from docs/todo/ to docs/done/, git mv'd to preserve history. Every cross-reference to the 12 moved files -- across the other moved docs themselves, graph-engineering-open-items.md, 2 Skill files, and 9 src/*.py docstrings/comments -- updated from docs/todo/<file> to docs/done/<file>. Verified no stale docs/todo/ references to any of the 12 filenames remain anywhere in the repo. graph-engineering-open-items.md itself stays in docs/todo/ (not moved) -- it's a living index that keeps gaining new entries from later comparison-note/gap-analysis passes (H itself was added this way, and a new item already appeared while this cleanup was in progress), not a single finished conclusion. Its own header now reflects that all of A/B/D/E/F/G/H are done and explains why it wasn't moved. Also fixed two pre-existing stray path references (missing todo/done/ prefix entirely, predating this cleanup) in its G section. Full src suite (625 tests) passes -- this is a pure documentation/comment change, no behavior touched. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Implements docs/todo/verifier-fan-out-jury-design.md. root_cause_trace.py: _tally_perspectives() extracts the existing >=2/3 rule out of judge_root_cause so the closure-based version and the new judge_root_cause_via_work_graph() share one implementation, not two that could drift apart. The fan-in vote stays plain Python (zero_token aggregation per the design-dynamic-work-graph Skill's own edge_type distinction) rather than becoming a fourth Work Node -- no reason to pay for an Agent call just to count votes. judge_root_cause_via_work_graph(): each perspective becomes an independent Work Node with real schema-constrained structured output ({"category", "detail"} directly), not real_validator_perspective's manual "CATEGORY:"/"DETAIL:" text-line parsing. judge_root_cause / real_validator_perspective are kept, not removed -- documented as the lightweight fallback for scenarios that don't need worktree/Work Graph overhead. org_level_loop.run_fix_loop (the one real production caller) now calls the Work Graph version; the fixer/verify calls are unchanged flat trigger_org_node calls. Real bug found and fixed along the way: this is the first production code path that actually triggers a run_graph() multi-node CONCURRENT layer (every graph_manifest before F was single-node or a strict serial chain, so G's ThreadPoolExecutor path had never really run in production). scheduler.py::run_goal_to_completion and task_execution.py::start_task_execution_in_background both created their conn without check_same_thread=False -- fixed both, since their conn can now reach run_graph()'s worker threads via run_fix_loop. Test boundary migrated in test_org_level_loop.py/test_scheduler.py: the 3 perspective calls are now mocked at work_graph_execute.write_workflow_script/ execute_work_graph (matching test_work_graph_orchestrate.py's pattern) instead of org_node_trigger.trigger_org_node. New tests cover: three real independent Work Node executions, judgment-rule equivalence with the closure version, clean per-node input_payload, and concurrent wall-clock overlap across the three perspectives. Full src suite (586 tests) + supervisor suite (125 tests) pass with zero regressions. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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run_fix_loop() chains U-015 (3-perspective root-cause judgment) + U-016 (routing) + real Coder/Planner/Validator calls into architecture doc §11's 4th MVP acceptance criterion: judge -> create bug_record -> route (fast_lane for category=coder, full_replan for category=planning -- a fixed mapping this Unit defines, since bug_record.suggested_route is technically an independent Validator judgment but REQ-05/architecture §11's scenarios always correlate the two, so no extra Agent call was added just to re-decide it) -> trigger the fixer -> re-trigger Validator -> close_task_ done on confirmed PASS. 3 new mocked stdlib unittest cases (route branching, verification-fails leaves the task out of 'done'). 160 total mocked tests across U-001-017, all passing. Real coverage reuses U-015's wall-collision scenario but this time drives an actual fix: a real Coder call edits collision.py in the repo, a real Validator call reads the fixed file and confirms it, running as a detached background process (survives this session's own restarts, unlike two earlier real runs this session that got silently orphaned by a session teardown with no completion record -- lesson learned, not repeated). This closes PH2-S1 (U-015/016/017): REQ-04/05/09 and architecture doc §11 criterion 4 are now real, verified code, not just planned intent. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>