fix: deep GPU integration, fix all ruff/mypy issues, add .dockerignore

- Integrate GPU scoring inline into reasoning/multi_path.py (auto-uses GPU when available)
- Integrate GPU deduplication into multi_agent/consensus_engine.py
- Add semantic_search() method to memory/semantic_graph.py with GPU acceleration
- Integrate GPU training into self_improvement/training.py AutoTrainer
- Fix all 758 ruff lint issues (whitespace, import sorting, unused imports, ambiguous vars, undefined names)
- Fix all 40 mypy type errors across the codebase (no-any-return, union-attr, arg-type, etc.)
- Fix deprecated ruff config keys (select/ignore -> [tool.ruff.lint])
- Add .dockerignore to exclude .venv/, tests/, docs/ from Docker builds
- Add type hints and docstrings to verification/outcome.py
- Fix E402 import ordering in witness_agent.py
- Fix F821 undefined names in vector_pgvector.py and native.py
- Fix E741 ambiguous variable names in reflective.py and recommender.py

All 276 tests pass. 0 ruff errors. 0 mypy errors.

Co-Authored-By: Nakamoto, S <defi@defi-oracle.io>

fusionagi/maa/tools.py

@@ -6,15 +6,14 @@ These tools generate actual manufacturing instructions:
 - machine_bind: Binds a design to a specific machine with capability validation
 """
 
-import json
 import uuid
 from typing import Any
 
 from pydantic import BaseModel, Field
 
+from fusionagi._logger import logger
 from fusionagi._time import utc_now_iso
 from fusionagi.tools.registry import ToolDef
-from fusionagi._logger import logger
 
 
 class GCodeOutput(BaseModel):
@@ -55,7 +54,7 @@ class MachineBindOutput(BaseModel):
 def _generate_gcode_header(machine_id: str, mpc_id: str) -> list[str]:
     """Generate standard G-code header."""
     return [
-        f"; G-code generated by FusionAGI MAA",
+        "; G-code generated by FusionAGI MAA",
         f"; MPC: {mpc_id}",
         f"; Machine: {machine_id}",
         f"; Generated: {utc_now_iso()}",
@@ -81,17 +80,17 @@ def _generate_gcode_footer() -> list[str]:
 def _generate_toolpath_gcode(toolpath_ref: str) -> list[str]:
     """
     Generate G-code from a toolpath reference.
-    
+
     In a real implementation, this would:
     1. Load the toolpath data from storage
     2. Convert toolpath segments to G-code commands
     3. Apply feed rates, spindle speeds, tool changes
-    
+
     For now, generates a representative sample.
     """
     # Parse toolpath reference for parameters
     # Format expected: "toolpath_{type}_{id}" or custom format
-    
+
     gcode_lines = [
         "; Toolpath: " + toolpath_ref,
         "",
@@ -106,7 +105,7 @@ def _generate_toolpath_gcode(toolpath_ref: str) -> list[str]:
         "",
         "; Begin cutting operations",
     ]
-    
+
     # Generate sample toolpath movements
     # In production, these would come from the actual toolpath data
     sample_moves = [
@@ -117,21 +116,21 @@ def _generate_toolpath_gcode(toolpath_ref: str) -> list[str]:
         "G1 Y0 ; Return Y",
         "G0 Z5.0 ; Retract",
     ]
-    
+
     gcode_lines.extend(sample_moves)
-    
+
     return gcode_lines
 
 
 def _cnc_emit_impl(mpc_id: str, machine_id: str, toolpath_ref: str) -> dict[str, Any]:
     """
     Generate CNC G-code for a manufacturing operation.
-    
+
     Args:
         mpc_id: Manufacturing Proof Certificate ID.
         machine_id: Target CNC machine identifier.
         toolpath_ref: Reference to toolpath data.
-    
+
     Returns:
         Dictionary with G-code and metadata.
     """
@@ -139,15 +138,15 @@ def _cnc_emit_impl(mpc_id: str, machine_id: str, toolpath_ref: str) -> dict[str,
         "CNC emit started",
         extra={"mpc_id": mpc_id, "machine_id": machine_id, "toolpath_ref": toolpath_ref},
     )
-    
+
     # Build G-code
     gcode_lines = []
     gcode_lines.extend(_generate_gcode_header(machine_id, mpc_id))
     gcode_lines.extend(_generate_toolpath_gcode(toolpath_ref))
     gcode_lines.extend(_generate_gcode_footer())
-    
+
     gcode = "\n".join(gcode_lines)
-    
+
     output = GCodeOutput(
         mpc_id=mpc_id,
         machine_id=machine_id,
@@ -159,24 +158,24 @@ def _cnc_emit_impl(mpc_id: str, machine_id: str, toolpath_ref: str) -> dict[str,
             "tool_changes": 1,
         },
     )
-    
+
     logger.info(
         "CNC emit completed",
         extra={"mpc_id": mpc_id, "line_count": len(gcode_lines)},
     )
-    
+
     return output.model_dump()
 
 
 def _am_slice_impl(mpc_id: str, machine_id: str, slice_ref: str) -> dict[str, Any]:
     """
     Generate AM slice instructions for additive manufacturing.
-    
+
     Args:
         mpc_id: Manufacturing Proof Certificate ID.
         machine_id: Target AM machine identifier.
         slice_ref: Reference to slice/geometry data.
-    
+
     Returns:
         Dictionary with slice data and metadata.
     """
@@ -184,18 +183,18 @@ def _am_slice_impl(mpc_id: str, machine_id: str, slice_ref: str) -> dict[str, An
         "AM slice started",
         extra={"mpc_id": mpc_id, "machine_id": machine_id, "slice_ref": slice_ref},
     )
-    
+
     # In production, this would:
     # 1. Load the geometry from slice_ref
     # 2. Apply slicing algorithm with machine-specific parameters
     # 3. Generate layer-by-layer toolpaths
     # 4. Calculate support structures if needed
-    
+
     # Generate representative slice data
     layer_height_mm = 0.2
     num_layers = 100  # Would be calculated from geometry height
-    
-    slice_data = {
+
+    slice_data: dict[str, Any] = {
         "format_version": "1.0",
         "machine_profile": machine_id,
         "settings": {
@@ -229,7 +228,7 @@ def _am_slice_impl(mpc_id: str, machine_id: str, slice_ref: str) -> dict[str, An
             "bounding_box_mm": {"x": 50, "y": 50, "z": num_layers * layer_height_mm},
         },
     }
-    
+
     output = SliceOutput(
         mpc_id=mpc_id,
         machine_id=machine_id,
@@ -241,23 +240,23 @@ def _am_slice_impl(mpc_id: str, machine_id: str, slice_ref: str) -> dict[str, An
             "estimated_time_minutes": slice_data["statistics"]["estimated_time_minutes"],
         },
     )
-    
+
     logger.info(
         "AM slice completed",
         extra={"mpc_id": mpc_id, "layer_count": num_layers},
     )
-    
+
     return output.model_dump()
 
 
 def _machine_bind_impl(mpc_id: str, machine_id: str) -> dict[str, Any]:
     """
     Bind a design (via MPC) to a specific machine.
-    
+
     Args:
         mpc_id: Manufacturing Proof Certificate ID.
         machine_id: Target machine identifier.
-    
+
     Returns:
         Dictionary with binding confirmation and validation results.
     """
@@ -265,16 +264,16 @@ def _machine_bind_impl(mpc_id: str, machine_id: str) -> dict[str, Any]:
         "Machine bind started",
         extra={"mpc_id": mpc_id, "machine_id": machine_id},
     )
-    
+
     # In production, this would:
     # 1. Load the MPC to get design requirements
     # 2. Load the machine profile
     # 3. Validate machine capabilities against design requirements
     # 4. Check envelope, tolerances, material compatibility
     # 5. Record the binding in the system
-    
+
     binding_id = f"binding_{mpc_id}_{machine_id}_{uuid.uuid4().hex[:8]}"
-    
+
     # Simulate capability validation
     capabilities_validated = True
     validation_results = {
@@ -283,7 +282,7 @@ def _machine_bind_impl(mpc_id: str, machine_id: str) -> dict[str, Any]:
         "material_check": {"status": "pass", "details": "Machine supports specified material"},
         "feature_check": {"status": "pass", "details": "Machine can produce required features"},
     }
-    
+
     output = MachineBindOutput(
         mpc_id=mpc_id,
         machine_id=machine_id,
@@ -294,24 +293,24 @@ def _machine_bind_impl(mpc_id: str, machine_id: str) -> dict[str, Any]:
             "validation_results": validation_results,
         },
     )
-    
+
     logger.info(
         "Machine bind completed",
         extra={"binding_id": binding_id, "validated": capabilities_validated},
     )
-    
+
     return output.model_dump()
 
 
 def cnc_emit_tool() -> ToolDef:
     """
     CNC G-code emission tool.
-    
+
     Generates G-code for CNC machining operations based on:
     - MPC: Manufacturing Proof Certificate with validated design
     - Machine: Target CNC machine configuration
     - Toolpath: Reference to toolpath data
-    
+
     Returns structured output with G-code and metadata.
     """
     return ToolDef(
@@ -336,13 +335,13 @@ def cnc_emit_tool() -> ToolDef:
 def am_slice_tool() -> ToolDef:
     """
     AM slice instruction tool.
-    
+
     Generates slice data for additive manufacturing operations:
     - Layer-by-layer toolpaths
     - Infill patterns
     - Support structure calculations
     - Machine-specific settings
-    
+
     Returns structured output with slice data and metadata.
     """
     return ToolDef(
@@ -367,12 +366,12 @@ def am_slice_tool() -> ToolDef:
 def machine_bind_tool() -> ToolDef:
     """
     Machine binding declaration tool.
-    
+
     Binds a design (via MPC) to a specific machine:
     - Validates machine capabilities against design requirements
     - Checks envelope, tolerances, material compatibility
     - Records the binding for audit trail
-    
+
     Returns structured output with binding confirmation.
     """
     return ToolDef(