Refactor inference engine and task management: Remove obsolete inference engine and ONNX engine files, update inference processing to utilize batch handling, and enhance task management structure in documentation. Adjust paths for task specifications to align with new directory organization.

.cursor/skills/autopilot/flows/existing-code.md

@@ -44,23 +44,23 @@ This step applies when the codebase was documented via the `/document` skill. Te
 ---
 
 **Step 3 — Decompose Tests**
-Condition: `_docs/02_document/tests/traceability-matrix.md` exists AND workspace contains source code files AND the autopilot state shows Document was run AND (`_docs/02_tasks/` does not exist or has no task files)
+Condition: `_docs/02_document/tests/traceability-matrix.md` exists AND workspace contains source code files AND the autopilot state shows Document was run AND (`_docs/02_tasks/todo/` does not exist or has no task files)
 
 Action: Read and execute `.cursor/skills/decompose/SKILL.md` in **tests-only mode** (pass `_docs/02_document/tests/` as input). The decompose skill will:
 1. Run Step 1t (test infrastructure bootstrap)
 2. Run Step 3 (blackbox test task decomposition)
 3. Run Step 4 (cross-verification against test coverage)
 
-If `_docs/02_tasks/` has some task files already, the decompose skill's resumability handles it.
+If `_docs/02_tasks/todo/` has some task files already, the decompose skill's resumability handles it.
 
 ---
 
 **Step 4 — Implement Tests**
-Condition: `_docs/02_tasks/` contains task files AND `_dependencies_table.md` exists AND the autopilot state shows Step 3 (Decompose Tests) is completed AND `_docs/03_implementation/FINAL_implementation_report.md` does not exist
+Condition: `_docs/02_tasks/todo/` contains task files AND `_docs/02_tasks/_dependencies_table.md` exists AND the autopilot state shows Step 3 (Decompose Tests) is completed AND `_docs/03_implementation/FINAL_implementation_report.md` does not exist
 
 Action: Read and execute `.cursor/skills/implement/SKILL.md`
 
-The implement skill reads test tasks from `_docs/02_tasks/` and implements them.
+The implement skill reads test tasks from `_docs/02_tasks/todo/` and implements them.
 
 If `_docs/03_implementation/` has batch reports, the implement skill detects completed tasks and continues.
 
@@ -91,16 +91,16 @@ Condition: the autopilot state shows Step 6 (Refactor) is completed AND the auto
 
 Action: Read and execute `.cursor/skills/new-task/SKILL.md`
 
-The new-task skill interactively guides the user through defining new functionality. It loops until the user is done adding tasks. New task files are written to `_docs/02_tasks/`.
+The new-task skill interactively guides the user through defining new functionality. It loops until the user is done adding tasks. New task files are written to `_docs/02_tasks/todo/`.
 
 ---
 
 **Step 8 — Implement**
-Condition: the autopilot state shows Step 7 (New Task) is completed AND `_docs/03_implementation/` does not contain a FINAL report covering the new tasks (check state for distinction between test implementation and feature implementation)
+Condition: the autopilot state shows Step 7 (New Task) is completed AND `_docs/02_tasks/todo/` contains task files AND `_docs/03_implementation/` does not contain a FINAL report covering the new tasks (check state for distinction between test implementation and feature implementation)
 
 Action: Read and execute `.cursor/skills/implement/SKILL.md`
 
-The implement skill reads the new tasks from `_docs/02_tasks/` and implements them. Tasks already implemented in Step 4 are skipped (the implement skill tracks completed tasks in batch reports).
+The implement skill reads the new tasks from `_docs/02_tasks/todo/` and implements them. Tasks already implemented in Step 4 are in `_docs/02_tasks/done/`.
 
 If `_docs/03_implementation/` has batch reports from this phase, the implement skill detects completed tasks and continues.