diff --git a/.env.example b/.env.example
deleted file mode 100644
index a3aba4e..0000000
--- a/.env.example
+++ /dev/null
@@ -1,17 +0,0 @@
-# Database Configuration
-HELIA_MONGO_URI=mongodb://localhost:27017
-HELIA_DATABASE_NAME=helia
-
-# S3 Configuration (MinIO or AWS)
-# Required for finding and downloading transcripts
-HELIA_S3_ENDPOINT=https://s3.amazonaws.com
-HELIA_S3_ACCESS_KEY=your_access_key
-HELIA_S3_SECRET_KEY=your_secret_key
-HELIA_S3_BUCKET=your-bucket-name
-HELIA_S3_REGION=us-east-1
-
-# LLM API Keys
-# These are used by the run configuration YAML via ${VAR} substitution
-OPENAI_API_KEY=sk-...
-ANTHROPIC_API_KEY=sk-ant-...
-OPENROUTER_API_KEY=sk-or-...
diff --git a/.gitignore b/.gitignore
index b525513..6e4e25d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,6 +7,7 @@ wheels/
 *.egg-info
 
 .env
+config.yaml
 
 # Virtual environments
 .venv
diff --git a/README.md b/README.md
index c5bc664..1cc6a94 100644
--- a/README.md
+++ b/README.md
@@ -17,7 +17,7 @@ src/helia/
 ├── analysis/
 │   └── extractor.py     # Metadata extraction (LLM-agnostic)
 ├── assessment/
-│   ├── core.py          # Clinical assessment logic (PHQ-8)
+│   └── core.py          # Clinical assessment logic (PHQ-8)
 │   └── schema.py        # Data models (AssessmentResult, PHQ8Item)
 ├── ingestion/
 │   └── parser.py        # Transcript parsing (DAIC-WOZ support)
@@ -50,6 +50,7 @@ graph TD
 -   **Clinical Parsing**: Native support for DAIC-WOZ transcript formats.
 -   **Structured Assessment**: Maps unstructured conversation to validatable PHQ-8 scores.
 -   **Document Persistence**: Stores full experimental context (config + evidence + scores) in MongoDB using Beanie.
+-   **Unified Configuration**: Single YAML config with environment variable fallbacks for system settings.
 
 ## Roadmap
 
@@ -67,22 +68,26 @@ uv sync
 
 ## Quick Start
 
-1.  **Environment Setup**:
+1.  **Configuration**:
+    Copy `example.config.yaml` to `config.yaml` and edit it.
     ```sh
-    export OPENAI_API_KEY=sk-...
-    # Ensure MongoDB is running (e.g., via Docker)
+    cp example.config.yaml config.yaml
     ```
+    
+    You can set system settings (MongoDB, S3) in the YAML file, or use environment variables (e.g., `HELIA_MONGO_URI`, `HELIA_S3_BUCKET`).
+    Provider API keys can be set in YAML or via `{PROVIDER_NAME}_API_KEY` (uppercased), e.g. `ANTHROPIC_API_KEY` for `providers.anthropic`.
 
 2.  **Run an Assessment**:
     ```sh
-    python -m helia.main "assess --input data/transcript.tsv"
+    # Ensure MongoDB is running
+    uv run python -m helia.main config.yaml
     ```
 
 ## Development
 
 -   **Linting**: `uv run ruff check .`
 -   **Formatting**: `uv run ruff format .`
--   **Type Checking**: `uv run pyrefly`
+-   **Type Checking**: `uv run ty check`
 
 ## License
 
diff --git a/example.run_config.yaml b/example.config.yaml
similarity index 55%
rename from example.run_config.yaml
rename to example.config.yaml
index d40ef54..e8b2f4f 100644
--- a/example.run_config.yaml
+++ b/example.config.yaml
@@ -1,25 +1,36 @@
-# Helia Run Configuration
-# This file defines the "providers" (LLM connections) and the "runs" (experiments).
-# Environment variables like ${OPENAI_API_KEY} are expanded at runtime.
+# System Configuration
+mongo_uri: "mongodb://localhost:27017"
+database_name: "helia"
+
+# S3 Configuration (MinIO or AWS)
+s3_endpoint: "https://s3.amazonaws.com"
+s3_access_key: "your_access_key"
+s3_secret_key: "your_secret_key"
+s3_bucket: "your-bucket-name"
+s3_prefix: ""
+s3_region: "us-east-1"
+
+# Run Configuration
+limit: 5
 
 providers:
   openai:
-    api_key: "${OPENAI_API_KEY}"
+    # Set api_key here or export OPENAI_API_KEY
     api_base: "https://api.openai.com/v1"
     api_format: "openai"
 
   anthropic:
-    api_key: "${ANTHROPIC_API_KEY}"
+    # Set api_key here or export ANTHROPIC_API_KEY
     api_base: "https://api.anthropic.com/v1"
     api_format: "anthropic"
 
   openrouter:
-    api_key: "${OPENROUTER_API_KEY}"
+    # Set api_key here or export OPENROUTER_API_KEY
     api_base: "https://openrouter.ai/api/v1"
     api_format: "openai"
 
   local_ollama:
-    api_key: "none"
+    # API key optional for local_* providers
     api_base: "http://localhost:11434/v1"
     api_format: "ollama"
 
@@ -37,6 +48,3 @@ runs:
       model_name: "llama3"
       temperature: 0.7
     prompt_id: "default"
-
-# Optional: Limit the number of transcripts processed
-limit: 5
diff --git a/run_config.yaml b/run_config.yaml
deleted file mode 100644
index 436f256..0000000
--- a/run_config.yaml
+++ /dev/null
@@ -1,15 +0,0 @@
-providers:
-  openrouter:
-    api_key: "${OPENROUTER_API_KEY}"
-    api_base: "https://openrouter.ai/api/v1"
-    api_format: "openai"
-
-runs:
-  - run_name: "gemini_flash"
-    model:
-      provider: openrouter
-      model_name: "google/gemini-3-flash-preview"
-      temperature: 1.0
-    prompt_id: "default"
-
-limit: 5
diff --git a/src/helia/agent/workflow.py b/src/helia/agent/workflow.py
index 9757904..b5d2b05 100644
--- a/src/helia/agent/workflow.py
+++ b/src/helia/agent/workflow.py
@@ -5,9 +5,6 @@ from typing import Any
 from langgraph.graph import END, StateGraph
 from pydantic import BaseModel
 
-from helia.llm.client import get_chat_model
-from helia.llm.settings import settings
-
 
 class AgentState(BaseModel):
     """State for the agent workflow."""
@@ -25,9 +22,8 @@ class AgentState(BaseModel):
 # proper protocol matching while maintaining runtime correctness.
 
 
-def planner_node(state: AgentState):  # noqa: ANN201
+def planner_node(state: AgentState):  # noqa: ANN201, ARG001
     """Plan the steps to answer the question."""
-    _ = state
     plan: list[str] = ["Understand question", "Retrieve info", "Synthesize answer"]
     return {"plan": plan}
 
@@ -57,40 +53,17 @@ def vector_tool_node(state: AgentState):  # noqa: ANN201
 def synthesizer_node(state: AgentState):  # noqa: ANN201
     """Synthesize an answer from the gathered context."""
     context_text = "\n".join(state.context)
-    question = state.question
 
-    prompt = f"""
-    Answer the user's question based on the provided context.
-
-    Context:
-    {context_text}
-
-    Question: {question}
-
-    Answer:
-    """
-
-    try:
-        llm = get_chat_model(
-            model_name=settings.model,
-            api_key=settings.resolve_api_key(),
-            base_url=settings.base_url,
-        )
-        messages = [
-            ("system", "You are a helpful assistant."),
-            ("user", prompt),
-        ]
-        response = llm.invoke(messages)
-        answer = str(response.content)
-    except Exception as e:
-        answer = f"Error generating answer: {e}. Fallback: Based on context: {context_text}, here is the answer."
+    answer = (
+        "Agent workflow is placeholder and no longer loads LLM settings from env vars. "
+        f"Fallback: Based on context: {context_text}, here is the answer."
+    )
 
     return {"answer": answer}
 
 
-def reflector_node(state: AgentState):  # noqa: ANN201
+def reflector_node(state: AgentState):  # noqa: ANN201, ARG001
     """Reflect on the quality of the answer."""
-    _ = state
     return {"critique": "Answer appears sufficient."}
 
 
diff --git a/src/helia/assessment/core.py b/src/helia/assessment/core.py
index a5068e1..ee9ec74 100644
--- a/src/helia/assessment/core.py
+++ b/src/helia/assessment/core.py
@@ -55,11 +55,10 @@ class PHQ8Evaluator:
         self.config = config
         self.parser = TranscriptParser()
 
-        # Initialize LangChain Chat Model
         self.llm = get_chat_model(
             model_name=self.config.model_name,
             api_key=self.config.api_key,
-            base_url=self.config.api_base,
+            base_url=self.config.api_base or "",
             temperature=self.config.temperature,
         )
 
diff --git a/src/helia/configuration.py b/src/helia/configuration.py
index 7fe3166..cafa67f 100644
--- a/src/helia/configuration.py
+++ b/src/helia/configuration.py
@@ -1,13 +1,18 @@
 from __future__ import annotations
 
 import os
-import re
-from pathlib import Path
-from typing import Literal, NamedTuple
+from typing import TYPE_CHECKING, Literal, NamedTuple
 
-import yaml
-from pydantic import BaseModel, Field, TypeAdapter
-from pydantic_settings import BaseSettings, SettingsConfigDict
+from pydantic import BaseModel, Field, model_validator
+from pydantic_settings import (
+    BaseSettings,
+    PydanticBaseSettingsSource,
+    SettingsConfigDict,
+    YamlConfigSettingsSource,
+)
+
+if TYPE_CHECKING:
+    from pathlib import Path
 
 
 class S3Config(NamedTuple):
@@ -21,42 +26,12 @@ class S3Config(NamedTuple):
     region_name: str | None = None
 
 
-class SystemConfig(BaseSettings):
-    """
-    System-level configuration loaded from environment variables.
-    Includes Database and AWS/S3 settings.
-    """
-
-    model_config = SettingsConfigDict(env_prefix="HELIA_", env_file=".env", extra="ignore")
-
-    mongo_uri: str = Field(..., description="MongoDB connection string")
-    database_name: str = Field("helia", description="MongoDB database name")
-
-    s3_endpoint: str = Field(..., description="S3 endpoint URL")
-    s3_access_key: str = Field(..., description="S3 access key")
-    s3_secret_key: str = Field(..., description="S3 secret key")
-    s3_bucket: str = Field(..., description="S3 bucket containing the dataset")
-    s3_prefix: str = Field("", description="S3 key prefix for dataset files")
-    s3_region: str | None = Field(None, description="S3 region name (optional)")
-
-    def get_s3_config(self) -> S3Config:
-        """Create an S3Config from the system configuration."""
-        return S3Config(
-            bucket_name=self.s3_bucket,
-            endpoint_url=self.s3_endpoint,
-            aws_access_key_id=self.s3_access_key,
-            aws_secret_access_key=self.s3_secret_key,
-            prefix=self.s3_prefix,
-            region_name=self.s3_region,
-        )
-
-
 class ProviderConfig(BaseModel):
     """
-    Configuration for an LLM provider
+    Configuration for an LLM provider.
     """
 
-    api_key: str
+    api_key: str | None = None
     api_base: str
     api_format: Literal["openai", "anthropic", "ollama"] = "openai"
 
@@ -81,50 +56,112 @@ class RunSpec(BaseModel):
     prompt_id: str = "default"
 
 
-class AssessBatchConfig(BaseModel):
+class HeliaConfig(BaseSettings):
     """
-    Configuration file structure for batch assessment.
+    Unified configuration for Helia.
+    Loads from YAML first, then falls back to Environment variables for system settings.
     """
 
-    providers: dict[str, ProviderConfig]
-    runs: list[RunSpec]
-    limit: int | None = None
+    # System Settings (Env Fallback available via HELIA_ prefix)
+    mongo_uri: str = Field(..., description="MongoDB connection string")
+    database_name: str = Field("helia", description="MongoDB database name")
+
+    s3_endpoint: str = Field(..., description="S3 endpoint URL")
+    s3_access_key: str = Field(..., description="S3 access key")
+    s3_secret_key: str = Field(..., description="S3 secret key")
+    s3_bucket: str = Field(..., description="S3 bucket containing the dataset")
+    s3_prefix: str = Field("", description="S3 key prefix for dataset files")
+    s3_region: str | None = Field(None, description="S3 region name (optional)")
+
+    # Run Settings
+    limit: int | None = Field(None, description="Limit the number of transcripts processed")
+    providers: dict[str, ProviderConfig] = Field(default_factory=dict)
+    runs: list[RunSpec] = Field(default_factory=list)
+
+    model_config = SettingsConfigDict(
+        env_prefix="HELIA_",
+        env_file=None,  # Disable .env file loading
+        extra="ignore",
+    )
+
+    def get_s3_config(self) -> S3Config:
+        """Create an S3Config from the system configuration."""
+        return S3Config(
+            bucket_name=self.s3_bucket,
+            endpoint_url=self.s3_endpoint,
+            aws_access_key_id=self.s3_access_key,
+            aws_secret_access_key=self.s3_secret_key,
+            prefix=self.s3_prefix,
+            region_name=self.s3_region,
+        )
+
+    @model_validator(mode="after")
+    def resolve_provider_api_keys(self) -> HeliaConfig:
+        """Resolve provider API keys from env vars as fallback.
+
+        - If `providers.<name>.api_key` is set in YAML, it is used.
+        - Otherwise, the loader tries `{NAME}_API_KEY` (uppercased provider name).
+        - Providers whose name starts with `local_` may omit an API key.
+        """
+        for name, provider in self.providers.items():
+            if provider.api_key:
+                continue
+
+            env_var_name = f"{name.upper()}_API_KEY"
+            if env_key := os.environ.get(env_var_name):
+                provider.api_key = env_key
+
+        return self
+
+    @model_validator(mode="after")
+    def validate_provider_api_keys(self) -> HeliaConfig:
+        """Enforce API key presence for non-local providers used by runs."""
+        used_providers = {run.model.provider for run in self.runs}
+
+        for provider_name in used_providers:
+            provider = self.providers.get(provider_name)
+            if provider is None:
+                msg = f"Provider '{provider_name}' is used in runs but not configured under 'providers'."
+                raise ValueError(msg)
+
+            if provider_name.startswith("local_"):
+                continue
+
+            if not provider.api_key:
+                env_var_name = f"{provider_name.upper()}_API_KEY"
+                msg = (
+                    f"Missing API key for provider '{provider_name}'. "
+                    f"Set providers.{provider_name}.api_key in YAML or export {env_var_name}."
+                )
+                raise ValueError(msg)
+
+        return self
 
 
-class AgentConfig(BaseModel):
-    # Placeholder for future agent config
-    command: Literal["agent"] = "agent"
 
 
-ConfigType = AssessBatchConfig
-
-
-def _expand_env_vars(yaml_content: str) -> str:
+def load_config(path: str | Path) -> HeliaConfig:
     """
-    Expand environment variables in the format ${VAR} or ${VAR:default}.
+    Load configuration from a YAML file, with environment variable fallback.
     """
-    pattern = re.compile(r"\$\{([^}^{]+)\}")
 
-    def replace(match: re.Match) -> str:
-        env_var = match.group(1)
-        default_value = ""
-        if ":" in env_var:
-            env_var, default_value = env_var.split(":", 1)
-        return os.environ.get(env_var, default_value)
+    # Create a dynamic subclass to bind the specific yaml_file path
+    class RuntimeHeliaConfig(HeliaConfig):
+        model_config = SettingsConfigDict(yaml_file=path)
 
-    return pattern.sub(replace, yaml_content)
+        @classmethod
+        def settings_customise_sources(
+            cls,
+            settings_cls: type[BaseSettings],
+            init_settings: PydanticBaseSettingsSource,  # noqa: ARG003
+            env_settings: PydanticBaseSettingsSource,
+            dotenv_settings: PydanticBaseSettingsSource,  # noqa: ARG003
+            file_secret_settings: PydanticBaseSettingsSource,  # noqa: ARG003
+        ) -> tuple[PydanticBaseSettingsSource, ...]:
+            return (
+                YamlConfigSettingsSource(settings_cls),
+                env_settings,
+                # No dotenv, no init_settings needed usually
+            )
 
-
-def load_config(path: str | Path) -> ConfigType:
-    with Path(path).open() as f:
-        content = f.read()
-
-    content = _expand_env_vars(content)
-    data = yaml.safe_load(content)
-
-    adapter = TypeAdapter(ConfigType)
-    return adapter.validate_python(data)
-
-
-def load_system_config() -> SystemConfig:
-    return SystemConfig()
+    return RuntimeHeliaConfig()  # type: ignore[call-arg]
diff --git a/src/helia/db.py b/src/helia/db.py
index 2edf920..180df87 100644
--- a/src/helia/db.py
+++ b/src/helia/db.py
@@ -8,10 +8,10 @@ from motor.motor_asyncio import AsyncIOMotorClient
 from helia.assessment.schema import AssessmentResult
 
 if TYPE_CHECKING:
-    from helia.configuration import SystemConfig
+    from helia.configuration import HeliaConfig
 
 
-async def init_db(config: SystemConfig) -> None:
+async def init_db(config: HeliaConfig) -> None:
     client = AsyncIOMotorClient(config.mongo_uri)
     await init_beanie(
         database=client[config.database_name],  # type: ignore[arg-type]
diff --git a/src/helia/llm/__init__.py b/src/helia/llm/__init__.py
index f1aa122..ea20460 100644
--- a/src/helia/llm/__init__.py
+++ b/src/helia/llm/__init__.py
@@ -1,4 +1,3 @@
-from helia.llm.client import get_openai_client
-from helia.llm.settings import settings
+from helia.llm.client import get_chat_model
 
-__all__ = ["get_openai_client", "settings"]
+__all__ = ["get_chat_model"]
diff --git a/src/helia/llm/client.py b/src/helia/llm/client.py
index 311b0d1..232bd72 100644
--- a/src/helia/llm/client.py
+++ b/src/helia/llm/client.py
@@ -3,55 +3,20 @@ from __future__ import annotations
 from typing import TYPE_CHECKING
 
 from langchain_openai import ChatOpenAI
-from openai import AsyncOpenAI, OpenAI
 from pydantic import SecretStr
 
-from helia.llm.settings import settings
-
 if TYPE_CHECKING:
     from langchain_core.language_models.chat_models import BaseChatModel
 
 
-def get_openai_client() -> OpenAI:
-    """
-    Returns an configured OpenAI client based on global settings.
-    Defaults to OpenRouter base_url if not specified otherwise.
-    """
-    api_key = settings.resolve_api_key()
-
-    return OpenAI(
-        base_url=settings.base_url,
-        api_key=api_key,
-        timeout=settings.timeout,
-        max_retries=settings.max_retries,
-    )
-
-
-def get_async_openai_client() -> AsyncOpenAI:
-    """
-    Returns a configured AsyncOpenAI client based on global settings.
-    """
-    api_key = settings.resolve_api_key()
-
-    return AsyncOpenAI(
-        base_url=settings.base_url,
-        api_key=api_key,
-        timeout=settings.timeout,
-        max_retries=settings.max_retries,
-    )
-
-
 def get_chat_model(
     model_name: str,
-    api_key: str | None = None,
-    base_url: str | None = None,
+    api_key: str | None,
+    base_url: str,
     temperature: float = 0.0,
     max_retries: int = 3,
 ) -> BaseChatModel:
-    """
-    Returns a configured LangChain ChatOpenAI instance.
-    Supports OpenRouter, Ollama, and OpenAI via base_url.
-    """
+    """Return a configured LangChain ChatOpenAI instance."""
     return ChatOpenAI(
         model_name=model_name,
         openai_api_key=SecretStr(api_key or ""),
diff --git a/src/helia/llm/settings.py b/src/helia/llm/settings.py
deleted file mode 100644
index 3c8cdb2..0000000
--- a/src/helia/llm/settings.py
+++ /dev/null
@@ -1,65 +0,0 @@
-import os
-from typing import Final
-
-from pydantic import Field
-from pydantic_settings import BaseSettings, SettingsConfigDict
-
-
-class LLMSettings(BaseSettings):
-    """
-    Configuration for LLM clients, defaulting to OpenRouter.
-    """
-
-    api_key: str | None = Field(
-        default=None,
-        description="API key for the LLM provider. Checks HELIA_LLM_API_KEY, OPENROUTER_API_KEY, then OPENAI_API_KEY.",
-    )
-    base_url: str = Field(
-        default="https://openrouter.ai/api/v1",
-        description="Base URL for the LLM provider. Defaults to OpenRouter.",
-    )
-    model: str = Field(
-        default="google/gemini-3.0-pro-preview",
-        description="Model identifier to use.",
-    )
-    timeout: float = Field(
-        default=30.0,
-        description="Request timeout in seconds.",
-    )
-    max_retries: int = Field(
-        default=2,
-        description="Maximum number of retries for failed requests.",
-    )
-
-    model_config = SettingsConfigDict(
-        env_prefix="HELIA_LLM_",
-        case_sensitive=False,
-        extra="ignore",
-    )
-
-    def resolve_api_key(self) -> str:
-        """
-        Resolves the API key with a fallback strategy:
-        1. configured api_key (from HELIA_LLM_API_KEY)
-        2. OPENROUTER_API_KEY env var
-        3. OPENAI_API_KEY env var
-        4. Raise ValueError if none found
-        """
-        if self.api_key:
-            return self.api_key
-
-        # Fallback 1: OpenRouter
-        if key := os.environ.get("OPENROUTER_API_KEY"):
-            return key
-
-        # Fallback 2: OpenAI
-        if key := os.environ.get("OPENAI_API_KEY"):
-            return key
-
-        raise ValueError(
-            "No API key found. Please set HELIA_LLM_API_KEY, OPENROUTER_API_KEY, or OPENAI_API_KEY."
-        )
-
-
-# Singleton instance for easy import
-settings: Final[LLMSettings] = LLMSettings()
diff --git a/src/helia/main.py b/src/helia/main.py
index 8131635..036e2ea 100644
--- a/src/helia/main.py
+++ b/src/helia/main.py
@@ -4,15 +4,13 @@ import logging
 from datetime import UTC, datetime
 from pathlib import Path
 
-from helia.agent.workflow import run_agent
 from helia.assessment.core import PHQ8Evaluator
 from helia.assessment.schema import RunConfig
 from helia.configuration import (
-    AssessBatchConfig,
+    HeliaConfig,
     RunSpec,
     S3Config,
     load_config,
-    load_system_config,
 )
 from helia.db import init_db
 from helia.ingestion.s3 import S3DatasetLoader
@@ -24,7 +22,7 @@ logger = logging.getLogger(__name__)
 async def process_run(
     run_spec: RunSpec,
     input_source: str,
-    run_config_data: AssessBatchConfig,
+    config: HeliaConfig,
     s3_config: S3Config,
     semaphore: asyncio.Semaphore,
 ) -> None:
@@ -34,11 +32,11 @@ async def process_run(
     async with semaphore:
         # Resolve Provider
         provider_name = run_spec.model.provider
-        if provider_name not in run_config_data.providers:
+        if provider_name not in config.providers:
             logger.error("Run %s refers to unknown provider %s", run_spec.run_name, provider_name)
             return
 
-        provider_config = run_config_data.providers[provider_name]
+        provider_config = config.providers[provider_name]
 
         # Download from S3 (Async)
         loader = S3DatasetLoader(s3_config)
@@ -111,61 +109,50 @@ async def main() -> None:
         return
 
     try:
-        run_config_data = load_config(config_path)
-        system_config = load_system_config()
+        config = load_config(config_path)
     except Exception:
         logger.exception("Error loading configuration")
         return
 
-    # Check the type of configuration
-    if isinstance(run_config_data, AssessBatchConfig):
-        # Run Pre-flight Checks
-        if not await check_all_connections(run_config_data, system_config):
-            logger.error("Pre-flight checks failed. Exiting.")
-            return
+    # Run Pre-flight Checks
+    if not await check_all_connections(config):
+        logger.error("Pre-flight checks failed. Exiting.")
+        return
 
-        # Ensure DB is initialized (redundant if pre-flight passed, but safe)
-        await init_db(system_config)
+    # Ensure DB is initialized (redundant if pre-flight passed, but safe)
+    await init_db(config)
 
-        # Create S3 config once and reuse
-        s3_config = system_config.get_s3_config()
+    # Create S3 config once and reuse
+    s3_config = config.get_s3_config()
 
-        # Discover transcripts (can remain sync or be made async, sync is fine for listing)
-        logger.info("Discovering transcripts in S3 bucket: %s", s3_config.bucket_name)
-        loader = S3DatasetLoader(s3_config)
-        keys = loader.list_transcripts()
+    # Discover transcripts (can remain sync or be made async, sync is fine for listing)
+    logger.info("Discovering transcripts in S3 bucket: %s", s3_config.bucket_name)
+    loader = S3DatasetLoader(s3_config)
+    keys = loader.list_transcripts()
 
-        # Apply limit if configured (Priority: CLI > Config)
-        limit = args.limit
-        limit = limit if limit is not None else run_config_data.limit
+    # Apply limit if configured (Priority: CLI > Config)
+    limit = args.limit
+    limit = limit if limit is not None else config.limit
 
-        if limit is not None:
-            logger.info("Limiting processing to first %d transcripts", limit)
-            keys = keys[:limit]
+    if limit is not None:
+        logger.info("Limiting processing to first %d transcripts", limit)
+        keys = keys[:limit]
 
-        # Create task list
-        tasks_data = [(run_spec, key) for run_spec in run_config_data.runs for key in keys]
-        logger.info("Starting batch assessment with %d total items...", len(tasks_data))
+    # Create task list
+    tasks_data = [(run_spec, key) for run_spec in config.runs for key in keys]
+    logger.info("Starting batch assessment with %d total items...", len(tasks_data))
 
-        # Limit concurrency to 10 parallel requests
-        semaphore = asyncio.Semaphore(10)
+    # Limit concurrency to 10 parallel requests
+    semaphore = asyncio.Semaphore(10)
 
-        tasks = [
-            process_run(run_spec, key, run_config_data, s3_config, semaphore)
-            for run_spec, key in tasks_data
-        ]
+    tasks = [
+        process_run(run_spec, key, config, s3_config, semaphore) for run_spec, key in tasks_data
+    ]
 
-        # Run all tasks concurrently
-        await asyncio.gather(*tasks)
+    # Run all tasks concurrently
+    await asyncio.gather(*tasks)
 
-        logger.info("Batch assessment complete.")
-
-    else:
-        # Agent command (Placeholder)
-        question = run_config_data.question
-        logger.info("\nRunning Re-Agent with question: '%s'\n", question)
-        result = run_agent(question)
-        logger.info(result["answer"])
+    logger.info("Batch assessment complete.")
 
 
 if __name__ == "__main__":
diff --git a/src/helia/preflight.py b/src/helia/preflight.py
index 88bd49d..1157264 100644
--- a/src/helia/preflight.py
+++ b/src/helia/preflight.py
@@ -10,12 +10,12 @@ from helia.db import init_db
 from helia.ingestion.s3 import S3DatasetLoader
 
 if TYPE_CHECKING:
-    from helia.configuration import AssessBatchConfig, ProviderConfig, S3Config, SystemConfig
+    from helia.configuration import HeliaConfig, ProviderConfig, S3Config
 
 logger = logging.getLogger(__name__)
 
 
-async def check_mongo(config: SystemConfig) -> bool:
+async def check_mongo(config: HeliaConfig) -> bool:
     """Verify MongoDB connectivity."""
     try:
         logger.info("Checking MongoDB connection...")
@@ -67,7 +67,7 @@ async def check_llm_provider(name: str, config: ProviderConfig, model_name: str)
         return True
 
 
-async def check_all_connections(run_config: AssessBatchConfig, system_config: SystemConfig) -> bool:
+async def check_all_connections(config: HeliaConfig) -> bool:
     """
     Run all pre-flight checks. Returns True if all checks pass.
     """
@@ -76,16 +76,16 @@ async def check_all_connections(run_config: AssessBatchConfig, system_config: Sy
     checks = []
 
     # 1. Check MongoDB
-    checks.append(check_mongo(system_config))
+    checks.append(check_mongo(config))
 
     # 2. Check S3
-    checks.append(check_s3(system_config.get_s3_config()))
+    checks.append(check_s3(config.get_s3_config()))
 
     # 3. Check All LLM Providers
-    for name, provider_config in run_config.providers.items():
+    for name, provider_config in config.providers.items():
         # Find a model used by this provider in the runs to use for the check
         model_name = next(
-            (run.model.model_name for run in run_config.runs if run.model.provider == name),
+            (run.model.model_name for run in config.runs if run.model.provider == name),
             None,
         )