feat: complete verified silicon local loop and final B consent

.github/workflows/test.yml

@@ -59,3 +59,45 @@ jobs:
 
       - name: Run frontend checks
         run: npm run check
+
+  silicon-local-loop:
+    name: Silicon local loop (public aidb bridge)
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    permissions:
+      contents: read
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          path: MatCreator
+      - name: Checkout pinned aidb integration dependency
+        uses: actions/checkout@v4
+        with:
+          repository: Zikkying/Ai-ready_Database
+          # Public bridge contract verified at this immutable integration commit.
+          # Published on codex/matcreator-ci-bridge; never use latest.
+          ref: 87148777fc9995a6d2e3bd85571ee8e20ff53181
+          path: Ai-ready_Database
+          persist-credentials: false
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+      - name: Install both public packages
+        run: |
+          python -m pip install --upgrade pip
+          python -m venv Ai-ready_Database/.venv
+          Ai-ready_Database/.venv/bin/python -m pip install -e ./Ai-ready_Database
+          python -m pip install -e ./MatCreator pytest
+      - name: Run isolated loop tests with zero skips
+        working-directory: MatCreator
+        env:
+          AI_READY_DB_ROOT: ${{ github.workspace }}/Ai-ready_Database
+          AI_READY_DB_PYTHON: ${{ github.workspace }}/Ai-ready_Database/.venv/bin/python
+        run: python script/check_silicon_loop.py tests --output .workspace/ci/silicon-check.json
+      - name: Retain failure and test artifacts
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: silicon-local-loop-results
+          path: MatCreator/.workspace/ci/
+          if-no-files-found: warn

AGENTS.md

@@ -0,0 +1,107 @@
+# AGENTS.md
+
+This file provides guidance to Qoder (qoder.com) when working with code in this repository.
+
+## Project Overview
+
+MatCreator is an agentic AI platform for computational materials science, built as an agent harness around the Google ADK runtime, a markdown-based skill library, a workspace, and a persistent knowledge graph. It offers CLI, API, and Web interfaces.
+
+## Commands
+
+### Environment setup
+
+```bash
+pip install uv
+uv venv .venv --python 3.12        # Python 3.12+ required (.python-version pins 3.12)
+source .venv/bin/activate
+uv pip install -e .                 # includes git deps (mat-bench, mat-know-base) — needs network
+```
+
+Frontend (only needed for Web UI development):
+
+```bash
+cd web/vite-frontend
+npm ci                              # Node.js >= 24.14.1 required (.nvmrc pins 24.14.1)
+```
+
+### Tests
+
+Backend (pytest; no pytest config file — run against `tests/` directly):
+
+```bash
+python -m pytest tests/ -v                        # full suite
+python -m pytest tests/test_ports_config.py -v    # single file
+python -m pytest tests/test_ports_config.py -k "name_pattern" -v   # single test
+```
+
+Note: CI (`.github/workflows/test.yml`) runs only a subset of test files plus the frontend check.
+
+Frontend:
+
+```bash
+cd web/vite-frontend
+npm run check          # runs node --test + vite build (this is what CI enforces)
+npm test               # node --test only
+npm run build          # vite build only
+```
+
+### Running
+
+```bash
+bash script/start_matcreator.sh    # Web UI: starts ADK API (:8000) + FastAPI (:8001) + Vite (:5173)
+matcreator chat --workspace .      # CLI, Flash mode (direct interaction)
+matcreator chat --workspace . --plan   # CLI, Plan mode (thinking agent -> execution graph -> execution agent)
+```
+
+The start script writes logs to `~/.matcreator/logs/{api-server,web-main,vite}.log` and resolves hosts/ports with precedence: environment variable > `~/.matcreator/config.yaml` > built-in default (logic in `src/matcreator/ports.py`).
+
+### Configuration
+
+Persistent settings live in `~/.matcreator/config.yaml` (relocatable via `MATCREATOR_HOME` or `MATCREATOR_CONFIG_PATH`):
+
+```bash
+matcreator config set llm.model=openai/qwen3-plus
+matcreator config set llm.api_key=your-api-key
+matcreator config set llm.base_url=https://api.example.com/v1
+matcreator config show
+```
+
+Precedence rule: in local mode pre-existing environment variables win over `config.yaml`; in server mode (`MATCREATOR_MODE=server`) `config.yaml` wins. Full reference including multi-model `llm.executor_cards`: `docs/configuration.md`.
+
+## Architecture
+
+Request flow (see `docs/architecture_components.md` for details):
+
+```
+Vite frontend (web/vite-frontend)  ->  FastAPI middleware (web/main.py)  ->  ADK API server  ->  MatCreator agent (src/matcreator)
+```
+
+### Layers
+
+- **Frontend** (`web/vite-frontend`): Vite app (Svelte + React mix, Ketcher, vis-network). Owns UI state, SSE consumption, and browser-reload reconnect to managed runs. Entry: `src/main.js`.
+- **FastAPI middleware** (`web/main.py`): the application backend. Two roles: (1) ADK protocol proxy (`/run_sse`, `/apps/*`, `/list-apps`); (2) MatCreator-specific APIs (sessions, workspace files, structures, skills, settings, cancellation). In server mode it also acts as a Docker worker control plane (one worker container per user). Managed runs are process-local — execution does not survive a middleware restart.
+- **Agent runtime** (`src/matcreator`): hosted on Google ADK. Entry `src/matcreator/agent.py`; CLI/API-server startup in `src/matcreator/scripts/start_agent.py`.
+
+### Agent internals
+
+- **Orchestrator** (`src/matcreator/agents/orchestrator/agent.py`): every turn starts with planning; if the planning agent approves an execution graph, control moves to the execution agent, which can return to planning within the same ADK invocation. Flash mode bypasses this loop.
+- **Thinking/execution agents** (`src/matcreator/agents/thinking_agent/`, `src/matcreator/agents/execution_agent/`): graph planning vs. step executors running tools/skills/remote jobs.
+- **Skills** (`src/matcreator/skills/`): modular markdown capabilities. Each skill is a directory with a `SKILL.md` carrying YAML frontmatter (`name`, `description`, `metadata.tools`, `metadata.dependent_skills`, `metadata.tags`). Skills declare dependencies on each other (e.g. `eos` depends on `ase`, `deepmd`, `bohrium`, ...).
+- **Knowledge** (`src/matcreator/knowledge/`): self-improving Know-Do Graph (extraction, review, migration, query) that accumulates experience across executions. Extraction/review frequency is configurable (`MATCREATOR_MEMORIZATION_FREQUENCY`, `MATCREATOR_REVIEW_FREQUENCY`; `0` disables).
+- **Control plane** (`src/matcreator/control_plane/`): durable remote-job store/service/monitor (E2B sandboxes), benchmark/evaluation runtime, worker supervisor.
+- **Workspace** (`src/matcreator/workspace.py`): sessions and artifacts live under the `--workspace` directory; ADK session state under `~/.matcreator/.adk/session.db`.
+
+### Source layout conventions
+
+- Python packages live under `src/matcreator` (`[tool.setuptools.packages.find] where = ["src"]`) — the import root is `src/`, not the repo root. `script/start_matcreator.sh` sets `PYTHONPATH` to `src/` so the checkout, not site-packages, is executed.
+- Skill files (`.md`, `.py`, `.yaml` under `skills/`) are shipped via `[tool.setuptools.package-data]` — new skill assets in those formats are packaged automatically.
+- Port/host resolution for all services is centralized in `src/matcreator/ports.py`.
+
+## Testing conventions
+
+- `tests/conftest.py` maintains `ALL_CONFIG_ENV_VARS`, the canonical list of configuration environment variables. When adding a new config env var to `src/matcreator/ports.py`, add it there so config-cleanup tests clear it automatically.
+- Frontend tests live in `web/vite-frontend/test/` and use the Node built-in test runner (`node --test`).
+
+## Docker
+
+Multi-stage build (`Dockerfile`): `worker` (API only, :8000), `control-plane` (API + built frontend, :8001), `local` (full dev image incl. Node, :8000/:8001/:5173). Port configuration via `.env` (see `.env.example`; copy to `.env` before `docker compose up`). Deployment docs: `docs/deployment/`.

CODING_STANDARDS.md

@@ -0,0 +1,10 @@
+# Scientific result review
+
+Review scientific feedback against the current structured tool receipt and retained calculation evidence. Automated receipt checks establish provenance and consistency; they do not establish the scientific accuracy of a narrative.
+
+- Check that the selected structures, calculation stages, methods, parameters, completion status and source jobs support the requested reuse. Explain material compatibility limits when they affect the answer.
+- Keep relaxation and static results distinct. State energy units and basis (for example eV per cell), and do not infer comparative physical meaning solely from a numerical difference between stages.
+- Assess accuracy and precision claims from convergence evidence, the model and method, and the intended use. Printed decimal places, a successful job, or a verified archive alone do not justify a claim such as “high precision.”
+- Keep retrieval defaults distinct from user requirements. A successful lookup is not permission to submit a calculation, and historical development policy A is not the current final B policy.
+
+The repeatable checks and evidence navigation are documented in [the silicon local-loop guide](docs/testing/silicon-local-loop.md).

docs/aidb_preflight_test_results.json

@@ -0,0 +1,108 @@
+{
+  "date": "2026-10-07",
+  "stage": "T1 development A",
+  "baseline_commit": "d92c7a2973831d5da5214befbc888e8587387eb4",
+  "baseline": {
+    "summary": "39 failed, 710 passed, 578 warnings in 41.51s",
+    "failures": [
+      "tests/test_benchmark_config.py::test_benchmark_client_registers_and_persists_missing_development_token",
+      "tests/test_disabled_skills.py::test_set_disabled_skill_names_updates_graph_nodes",
+      "tests/test_evaluation_routes.py::test_toggle_skill_graph_node_updates_and_reports_graph_state",
+      "tests/test_kdg_extractor.py::test_extractor_advances_cursor_for_empty_valid_response",
+      "tests/test_kdg_extractor.py::test_extractor_migrates_legacy_extracted_session",
+      "tests/test_kdg_extractor.py::test_extractor_skips_unchanged_session_and_processes_only_delta",
+      "tests/test_kdg_progressive_retrieval.py::test_graph_agent_tool_routes_through_protected_reviewer_policy",
+      "tests/test_kdg_progressive_retrieval.py::test_graph_agent_tool_scopes_memory_review_to_current_session",
+      "tests/test_kdg_progressive_retrieval.py::test_graph_disabled_skills_are_hidden_from_discovery_and_reads",
+      "tests/test_skill_graph_seed.py::test_seed_removes_stale_managed_skill_and_uses_virtual_dependency",
+      "tests/test_skill_graph_seed.py::test_seed_reuses_disabled_skill_node_and_merges_legacy_duplicate",
+      "tests/test_step_executor_runner.py::test_step_executor_retries_only_malformed_streamed_tool_arguments",
+      "tests/test_structure_modeling.py::test_crystal_is_created_through_matcraft_bulk_builder",
+      "tests/test_structure_modeling.py::test_matcraft_perturbation_is_seeded_and_changes_positions",
+      "tests/test_structure_modeling.py::test_molecule_can_be_created_or_appended",
+      "tests/test_structure_modeling.py::test_smiles_molecule_can_be_appended_at_requested_center",
+      "tests/test_structure_modeling.py::test_supercell_supports_general_integer_matrix",
+      "tests/test_web_concurrent_sessions.py::test_active_session_transitions_recompute_composer_state",
+      "tests/test_web_concurrent_sessions.py::test_all_chat_disclosures_share_the_reading_position_controller",
+      "tests/test_web_concurrent_sessions.py::test_bottom_attachment_and_node_toggle_use_one_scroll_policy",
+      "tests/test_web_concurrent_sessions.py::test_chat_messages_use_one_model_scheduler_and_stable_regions",
+      "tests/test_web_concurrent_sessions.py::test_completed_request_handoffs_live_turn_before_durable_refresh",
+      "tests/test_web_concurrent_sessions.py::test_frontend_tracks_requests_per_session",
+      "tests/test_web_concurrent_sessions.py::test_image_and_all_timeline_updates_preserve_node_disclosures",
+      "tests/test_web_concurrent_sessions.py::test_new_session_ids_are_not_limited_to_one_second_resolution",
+      "tests/test_web_concurrent_sessions.py::test_plain_text_blocks_keep_history_order_and_stable_identity",
+      "tests/test_web_concurrent_sessions.py::test_remote_job_polling_is_scoped_to_the_active_session",
+      "tests/test_web_concurrent_sessions.py::test_remote_jobs_are_collapsed_and_keep_lifecycle_status_visible",
+      "tests/test_web_concurrent_sessions.py::test_reselecting_the_active_session_does_not_rebuild_the_view",
+      "tests/test_web_concurrent_sessions.py::test_roadmap_fits_after_the_popup_has_a_stable_layout",
+      "tests/test_web_concurrent_sessions.py::test_running_session_switch_discovers_and_reconnects_managed_run",
+      "tests/test_web_concurrent_sessions.py::test_session_creation_does_not_start_knowledge_review",
+      "tests/test_web_concurrent_sessions.py::test_session_switch_loads_page_scoped_graph_after_the_transcript_page",
+      "tests/test_web_concurrent_sessions.py::test_session_switch_renders_cached_snapshot_immediately",
+      "tests/test_web_concurrent_sessions.py::test_sse_request_uses_captured_session_context",
+      "tests/test_web_concurrent_sessions.py::test_startup_keeps_session_api_ready_while_maintenance_runs_in_background",
+      "tests/test_web_concurrent_sessions.py::test_startup_restores_only_an_accessible_session_owner_tuple",
+      "tests/test_web_concurrent_sessions.py::test_step_cancellation_identifies_the_active_session_owner",
+      "tests/test_web_concurrent_sessions.py::test_stop_and_plan_refreshes_preserve_open_node_dialogs"
+    ]
+  },
+  "final": {
+    "summary": "39 failed, 743 passed, 585 warnings in 61.57s (0:01:01)",
+    "failures": [
+      "tests/test_benchmark_config.py::test_benchmark_client_registers_and_persists_missing_development_token",
+      "tests/test_disabled_skills.py::test_set_disabled_skill_names_updates_graph_nodes",
+      "tests/test_evaluation_routes.py::test_toggle_skill_graph_node_updates_and_reports_graph_state",
+      "tests/test_kdg_extractor.py::test_extractor_advances_cursor_for_empty_valid_response",
+      "tests/test_kdg_extractor.py::test_extractor_migrates_legacy_extracted_session",
+      "tests/test_kdg_extractor.py::test_extractor_skips_unchanged_session_and_processes_only_delta",
+      "tests/test_kdg_progressive_retrieval.py::test_graph_agent_tool_routes_through_protected_reviewer_policy",
+      "tests/test_kdg_progressive_retrieval.py::test_graph_agent_tool_scopes_memory_review_to_current_session",
+      "tests/test_kdg_progressive_retrieval.py::test_graph_disabled_skills_are_hidden_from_discovery_and_reads",
+      "tests/test_skill_graph_seed.py::test_seed_removes_stale_managed_skill_and_uses_virtual_dependency",
+      "tests/test_skill_graph_seed.py::test_seed_reuses_disabled_skill_node_and_merges_legacy_duplicate",
+      "tests/test_step_executor_runner.py::test_step_executor_retries_only_malformed_streamed_tool_arguments",
+      "tests/test_structure_modeling.py::test_crystal_is_created_through_matcraft_bulk_builder",
+      "tests/test_structure_modeling.py::test_matcraft_perturbation_is_seeded_and_changes_positions",
+      "tests/test_structure_modeling.py::test_molecule_can_be_created_or_appended",
+      "tests/test_structure_modeling.py::test_smiles_molecule_can_be_appended_at_requested_center",
+      "tests/test_structure_modeling.py::test_supercell_supports_general_integer_matrix",
+      "tests/test_web_concurrent_sessions.py::test_active_session_transitions_recompute_composer_state",
+      "tests/test_web_concurrent_sessions.py::test_all_chat_disclosures_share_the_reading_position_controller",
+      "tests/test_web_concurrent_sessions.py::test_bottom_attachment_and_node_toggle_use_one_scroll_policy",
+      "tests/test_web_concurrent_sessions.py::test_chat_messages_use_one_model_scheduler_and_stable_regions",
+      "tests/test_web_concurrent_sessions.py::test_completed_request_handoffs_live_turn_before_durable_refresh",
+      "tests/test_web_concurrent_sessions.py::test_frontend_tracks_requests_per_session",
+      "tests/test_web_concurrent_sessions.py::test_image_and_all_timeline_updates_preserve_node_disclosures",
+      "tests/test_web_concurrent_sessions.py::test_new_session_ids_are_not_limited_to_one_second_resolution",
+      "tests/test_web_concurrent_sessions.py::test_plain_text_blocks_keep_history_order_and_stable_identity",
+      "tests/test_web_concurrent_sessions.py::test_remote_job_polling_is_scoped_to_the_active_session",
+      "tests/test_web_concurrent_sessions.py::test_remote_jobs_are_collapsed_and_keep_lifecycle_status_visible",
+      "tests/test_web_concurrent_sessions.py::test_reselecting_the_active_session_does_not_rebuild_the_view",
+      "tests/test_web_concurrent_sessions.py::test_roadmap_fits_after_the_popup_has_a_stable_layout",
+      "tests/test_web_concurrent_sessions.py::test_running_session_switch_discovers_and_reconnects_managed_run",
+      "tests/test_web_concurrent_sessions.py::test_session_creation_does_not_start_knowledge_review",
+      "tests/test_web_concurrent_sessions.py::test_session_switch_loads_page_scoped_graph_after_the_transcript_page",
+      "tests/test_web_concurrent_sessions.py::test_session_switch_renders_cached_snapshot_immediately",
+      "tests/test_web_concurrent_sessions.py::test_sse_request_uses_captured_session_context",
+      "tests/test_web_concurrent_sessions.py::test_startup_keeps_session_api_ready_while_maintenance_runs_in_background",
+      "tests/test_web_concurrent_sessions.py::test_startup_restores_only_an_accessible_session_owner_tuple",
+      "tests/test_web_concurrent_sessions.py::test_step_cancellation_identifies_the_active_session_owner",
+      "tests/test_web_concurrent_sessions.py::test_stop_and_plan_refreshes_preserve_open_node_dialogs"
+    ]
+  },
+  "new_failures": [],
+  "resolved_baseline_failures": [],
+  "collection_errors_reproduced_at_baseline": [
+    "tests/test_execution_grouping.py",
+    "tests/test_matcreator_phase_and_skills.py"
+  ],
+  "focused_tests": {
+    "passed": 40,
+    "failed": 0
+  },
+  "aidb_bridge_tests": {
+    "passed": 14,
+    "failed": 0
+  },
+  "real_calculation_submitted": false
+}