refactor: remove dead ports, config models, factory shim, JSON helper

Delete vestigial port contracts (SecretsProvider/WorkflowSerializer/
CacheProtocol + duplicate ModelProvider), unread config models/flags
(Prompt* trio, deep_extraction_*, interrogation_rounds), the llm.factory
re-export shim, select_model_with_highest_context alias, the dead
extract_json_from_text extractor, and two empty application packages.

Claude-Session: https://claude.ai/code/session_01KGUEXHcGDrqkCGPz7Y1G88

Author: nikolay-e

src/certamen/application/serialization/__init__.py

@@ -39,7 +39,7 @@ class BaseNode(DomainBaseNode):
     async def ensure_models_or_empty(
         self, models_input: Any, single: bool = False
     ) -> tuple[dict[str, Any], dict[str, Any] | None]:
-        from certamen.infrastructure.llm.factory import (
+        from certamen.infrastructure.llm.model_factory import (
             ensure_model_instances,
             ensure_single_model_instance,
         )

src/certamen/application/services/__init__.py

@@ -66,7 +66,7 @@ async def execute(
         from certamen.domain.disagreement.detector import (
             DisagreementDetector,
         )
-        from certamen.infrastructure.llm.factory import (
+        from certamen.infrastructure.llm.model_factory import (
             ensure_single_model_instance,
         )
 

src/certamen/application/workflow/nodes/base.py

@@ -11,7 +11,7 @@
 )
 from certamen.application.workflow.registry import register_node
 from certamen.infrastructure.config.env import get_ollama_base_url
-from certamen.infrastructure.llm.factory import (
+from certamen.infrastructure.llm.model_factory import (
     ensure_single_model_instance,
 )
 from certamen.infrastructure.llm.registry import ProviderRegistry

src/certamen/application/workflow/nodes/disagreement.py

@@ -5,7 +5,6 @@
     PROMPTS,
     RETRY,
     get_defaults,
-    select_model_with_highest_context,
 )
 from certamen.infrastructure.config.env import (
     get_bool_env,
@@ -29,6 +28,5 @@
     "get_int_env",
     "get_ollama_base_url",
     "get_str_env",
-    "select_model_with_highest_context",
     "validate_config",
 ]

src/certamen/application/workflow/nodes/llm.py

@@ -1,12 +1,5 @@
 from typing import Any
 
-from certamen.domain.model_selection import select_model_by_capacity
-
-
-def select_model_with_highest_context(models: dict[str, Any]) -> str | None:
-    return select_model_by_capacity(models, include_max_tokens=False)
-
-
 # Models are discovered dynamically from LiteLLM and Ollama API.
 # For Ollama: queries local server at OLLAMA_BASE_URL/api/tags
 # For cloud providers: uses litellm.models_by_provider as source of truth
@@ -35,11 +28,8 @@ def select_model_with_highest_context(models: dict[str, Any]) -> str | None:
     "disagreement_investigation_enabled": True,  # Deep-dive into model disagreements
     "confidence_calibration_enabled": True,  # Append confidence tags to initial prompts
     "knowledge_map_enabled": True,  # Build structured knowledge map after tournament
-    "deep_extraction_enabled": False,  # Recursive sub-tournaments on exploration branches (expensive)
-    "deep_extraction_depth": 2,  # Max recursion depth for deep extraction
     "persistence_enabled": True,  # Persist knowledge maps to SQLite across tournaments
     "persistence_db_path": "certamen_knowledge.db",  # Path to knowledge store database
-    "interrogation_rounds": 1,  # Number of interrogation rounds (round 2 probes round 1 findings)
 }
 
 # Default prompts (JSON-like structured format)

src/certamen/infrastructure/config/__init__.py

@@ -24,8 +24,6 @@ class FeaturesConfig(BaseModel):
     disagreement_investigation_enabled: bool = True
     confidence_calibration_enabled: bool = True
     knowledge_map_enabled: bool = True
-    deep_extraction_enabled: bool = False
-    deep_extraction_depth: int = 2
     persistence_enabled: bool = True
     persistence_db_path: str = "certamen_knowledge.db"
 
@@ -36,24 +34,6 @@ class KnowledgeBankConfig(BaseModel):
     max_insights: int = Field(default=100, ge=1)
 
 
-class PromptMetadata(BaseModel):
-    version: str = "1.0"
-    type: str = "instruction"
-    phase: str
-
-
-class PromptConfig(BaseModel):
-    content: str
-    metadata: PromptMetadata
-
-
-class PromptsConfig(BaseModel):
-    initial: PromptConfig
-    feedback: PromptConfig
-    improvement: PromptConfig
-    evaluate: PromptConfig
-
-
 class ModelConfig(BaseModel):
     model_config = {"extra": "allow"}
 

src/certamen/infrastructure/config/defaults.py

@@ -1,8 +1,8 @@
-from certamen.infrastructure.llm.factory import (
+from certamen.infrastructure.llm.litellm_adapter import LiteLLMModel
+from certamen.infrastructure.llm.model_factory import (
     ensure_model_instances,
     ensure_single_model_instance,
 )
-from certamen.infrastructure.llm.litellm_adapter import LiteLLMModel
 from certamen.infrastructure.llm.registry import ProviderRegistry
 from certamen.infrastructure.llm.retry import run_with_retry