diff --git a/README.md b/README.md
index e374b79c..99637f64 100644
--- a/README.md
+++ b/README.md
@@ -84,10 +84,10 @@ To customize settings, create a `haiku.rag.yaml` config file (see [Configuration
 ## Python Usage
 
 ```python
-from haiku.rag.agui.stream import stream_graph
 from haiku.rag.client import HaikuRAG
 from haiku.rag.config import Config
-from haiku.rag.research import (
+from haiku.rag.graph.agui import stream_graph
+from haiku.rag.graph.research import (
     ResearchContext,
     ResearchDeps,
     ResearchState,
diff --git a/docs/agents.md b/docs/agents.md
index 73355100..08b7cf6b 100644
--- a/docs/agents.md
+++ b/docs/agents.md
@@ -96,9 +96,9 @@ Python usage:
 ```python
 from haiku.rag.client import HaikuRAG
 from haiku.rag.config import Config
-from haiku.rag.qa.deep.dependencies import DeepQAContext
-from haiku.rag.qa.deep.graph import build_deep_qa_graph
-from haiku.rag.qa.deep.state import DeepQADeps, DeepQAState
+from haiku.rag.graph.deep_qa.dependencies import DeepQAContext
+from haiku.rag.graph.deep_qa.graph import build_deep_qa_graph
+from haiku.rag.graph.deep_qa.state import DeepQADeps, DeepQAState
 
 async with HaikuRAG(path_to_db) as client:
     # Use global config (recommended)
@@ -205,9 +205,9 @@ Python usage (blocking result):
 ```python
 from haiku.rag.client import HaikuRAG
 from haiku.rag.config import Config
-from haiku.rag.research.dependencies import ResearchContext
-from haiku.rag.research.graph import build_research_graph
-from haiku.rag.research.state import ResearchDeps, ResearchState
+from haiku.rag.graph.research.dependencies import ResearchContext
+from haiku.rag.graph.research.graph import build_research_graph
+from haiku.rag.graph.research.state import ResearchDeps, ResearchState
 
 async with HaikuRAG(path_to_db) as client:
     # Use global config (recommended)
@@ -253,12 +253,12 @@ result = await graph.run(state=state, deps=deps)
 Python usage (streamed AG-UI events):
 
 ```python
-from haiku.rag.agui.stream import stream_graph
+from haiku.rag.graph.agui import stream_graph
 from haiku.rag.client import HaikuRAG
 from haiku.rag.config import Config
-from haiku.rag.research.dependencies import ResearchContext
-from haiku.rag.research.graph import build_research_graph
-from haiku.rag.research.state import ResearchDeps, ResearchState
+from haiku.rag.graph.research.dependencies import ResearchContext
+from haiku.rag.graph.research.graph import build_research_graph
+from haiku.rag.graph.research.state import ResearchDeps, ResearchState
 
 async with HaikuRAG(path_to_db) as client:
     graph = build_research_graph(config=Config)
diff --git a/docs/cli.md b/docs/cli.md
index 9f433cd7..b47c2587 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -162,7 +162,7 @@ Research parameters like `max_iterations`, `confidence_threshold`, and `max_conc
 
 When `--verbose` is set, the CLI consumes the research graph's AG-UI event stream, displaying step events and activity snapshots as agents progress through planning, search, evaluation, and synthesis. Without `--verbose`, only the final research report is displayed.
 
-If you build your own integration, import `stream_graph` from `haiku.rag.agui.stream` to access AG-UI events (`STEP_STARTED`, `ACTIVITY_SNAPSHOT`, `STATE_SNAPSHOT`, `RUN_FINISHED`, etc.) and render them however you like while the graph is running.
+If you build your own integration, import `stream_graph` from `haiku.rag.graph.agui` to access AG-UI events (`STEP_STARTED`, `ACTIVITY_SNAPSHOT`, `STATE_SNAPSHOT`, `RUN_FINISHED`, etc.) and render them however you like while the graph is running.
 
 ## Server
 
diff --git a/examples/a2a-server/haiku_rag_a2a/a2a/__init__.py b/examples/a2a-server/haiku_rag_a2a/a2a/__init__.py
index 03af95ab..d06eaae9 100644
--- a/examples/a2a-server/haiku_rag_a2a/a2a/__init__.py
+++ b/examples/a2a-server/haiku_rag_a2a/a2a/__init__.py
@@ -6,7 +6,7 @@ import logfire
 from pydantic_ai import Agent, RunContext
 
 from haiku.rag.config import AppConfig, Config
-from haiku.rag.graph_common import get_model
+from haiku.rag.graph.common import get_model
 
 from .context import load_message_history, save_message_history
 from .models import A2AConfig, AgentDependencies, SearchResult
diff --git a/examples/ag-ui-research/backend/agent.py b/examples/ag-ui-research/backend/agent.py
index 5362696a..049e0dbd 100644
--- a/examples/ag-ui-research/backend/agent.py
+++ b/examples/ag-ui-research/backend/agent.py
@@ -8,7 +8,7 @@ from pydantic_ai.ag_ui import StateDeps
 
 from haiku.rag.client import HaikuRAG
 from haiku.rag.config import Config
-from haiku.rag.graph_common import get_model
+from haiku.rag.graph.common import get_model
 
 
 class ResearchState(BaseModel):
diff --git a/haiku_rag_slim/haiku/rag/app.py b/haiku_rag_slim/haiku/rag/app.py
index 1ce07208..ba2e77c3 100644
--- a/haiku_rag_slim/haiku/rag/app.py
+++ b/haiku_rag_slim/haiku/rag/app.py
@@ -8,14 +8,14 @@ from rich.console import Console
 from rich.markdown import Markdown
 from rich.progress import Progress
 
-from haiku.rag.agui import AGUIConsoleRenderer, stream_graph
 from haiku.rag.client import HaikuRAG
 from haiku.rag.config import AppConfig, Config
+from haiku.rag.graph.agui import AGUIConsoleRenderer, stream_graph
+from haiku.rag.graph.research.dependencies import ResearchContext
+from haiku.rag.graph.research.graph import build_research_graph
+from haiku.rag.graph.research.state import ResearchDeps, ResearchState
 from haiku.rag.mcp import create_mcp_server
 from haiku.rag.monitor import FileWatcher
-from haiku.rag.research.dependencies import ResearchContext
-from haiku.rag.research.graph import build_research_graph
-from haiku.rag.research.state import ResearchDeps, ResearchState
 from haiku.rag.store.models.chunk import Chunk
 from haiku.rag.store.models.document import Document
 
@@ -216,9 +216,9 @@ class HaikuRAGApp:
         async with HaikuRAG(db_path=self.db_path, config=self.config) as self.client:
             try:
                 if deep:
-                    from haiku.rag.qa.deep.dependencies import DeepQAContext
-                    from haiku.rag.qa.deep.graph import build_deep_qa_graph
-                    from haiku.rag.qa.deep.state import DeepQADeps, DeepQAState
+                    from haiku.rag.graph.deep_qa.dependencies import DeepQAContext
+                    from haiku.rag.graph.deep_qa.graph import build_deep_qa_graph
+                    from haiku.rag.graph.deep_qa.state import DeepQADeps, DeepQAState
 
                     graph = build_deep_qa_graph(config=self.config)
                     context = DeepQAContext(
@@ -229,7 +229,7 @@ class HaikuRAGApp:
 
                     if verbose:
                         # Use AG-UI renderer to process and display events
-                        from haiku.rag.agui import AGUIConsoleRenderer
+                        from haiku.rag.graph.agui import AGUIConsoleRenderer
 
                         renderer = AGUIConsoleRenderer(self.console)
                         result_dict = await renderer.render(
@@ -287,7 +287,7 @@ class HaikuRAGApp:
                     return
 
                 # Convert dict to ResearchReport model
-                from haiku.rag.research.models import ResearchReport
+                from haiku.rag.graph.research.models import ResearchReport
 
                 report = ResearchReport.model_validate(report_dict)
 
@@ -497,7 +497,7 @@ class HaikuRAGApp:
                 async def run_agui():
                     import uvicorn
 
-                    from haiku.rag.agui import create_agui_server
+                    from haiku.rag.graph.agui import create_agui_server
 
                     logger.info(
                         f"Starting AG-UI server on {self.config.agui.host}:{self.config.agui.port}"
diff --git a/haiku_rag_slim/haiku/rag/graph/__init__.py b/haiku_rag_slim/haiku/rag/graph/__init__.py
new file mode 100644
index 00000000..fff8e10a
--- /dev/null
+++ b/haiku_rag_slim/haiku/rag/graph/__init__.py
@@ -0,0 +1,26 @@
+"""Graph module for haiku.rag.
+
+This module contains all graph-related functionality including:
+- AG-UI protocol for graph streaming
+- Common graph utilities and models
+- Research graph implementation
+- Deep QA graph implementation
+"""
+
+from haiku.rag.graph.agui import (
+    AGUIConsoleRenderer,
+    AGUIEmitter,
+    create_agui_server,
+    stream_graph,
+)
+from haiku.rag.graph.deep_qa.graph import build_deep_qa_graph
+from haiku.rag.graph.research.graph import build_research_graph
+
+__all__ = [
+    "AGUIConsoleRenderer",
+    "AGUIEmitter",
+    "build_deep_qa_graph",
+    "build_research_graph",
+    "create_agui_server",
+    "stream_graph",
+]
diff --git a/haiku_rag_slim/haiku/rag/agui/__init__.py b/haiku_rag_slim/haiku/rag/graph/agui/__init__.py
similarity index 76%
rename from haiku_rag_slim/haiku/rag/agui/__init__.py
rename to haiku_rag_slim/haiku/rag/graph/agui/__init__.py
index fab7a016..7259a6b0 100644
--- a/haiku_rag_slim/haiku/rag/agui/__init__.py
+++ b/haiku_rag_slim/haiku/rag/graph/agui/__init__.py
@@ -1,8 +1,8 @@
 """Generic AG-UI protocol support for haiku.rag graphs."""
 
-from haiku.rag.agui.cli_renderer import AGUIConsoleRenderer
-from haiku.rag.agui.emitter import AGUIEmitter
-from haiku.rag.agui.events import (
+from haiku.rag.graph.agui.cli_renderer import AGUIConsoleRenderer
+from haiku.rag.graph.agui.emitter import AGUIEmitter
+from haiku.rag.graph.agui.events import (
     AGUIEvent,
     emit_activity,
     emit_activity_delta,
@@ -18,14 +18,14 @@ from haiku.rag.agui.events import (
     emit_text_message_end,
     emit_text_message_start,
 )
-from haiku.rag.agui.server import (
+from haiku.rag.graph.agui.server import (
     RunAgentInput,
     create_agui_app,
     create_agui_server,
     format_sse_event,
 )
-from haiku.rag.agui.state import compute_state_delta
-from haiku.rag.agui.stream import stream_graph
+from haiku.rag.graph.agui.state import compute_state_delta
+from haiku.rag.graph.agui.stream import stream_graph
 
 __all__ = [
     "AGUIConsoleRenderer",
diff --git a/haiku_rag_slim/haiku/rag/agui/cli_renderer.py b/haiku_rag_slim/haiku/rag/graph/agui/cli_renderer.py
similarity index 99%
rename from haiku_rag_slim/haiku/rag/agui/cli_renderer.py
rename to haiku_rag_slim/haiku/rag/graph/agui/cli_renderer.py
index c09e62b6..52e223dc 100644
--- a/haiku_rag_slim/haiku/rag/agui/cli_renderer.py
+++ b/haiku_rag_slim/haiku/rag/graph/agui/cli_renderer.py
@@ -5,7 +5,7 @@ from typing import Any
 
 from rich.console import Console
 
-from haiku.rag.agui.events import AGUIEvent
+from haiku.rag.graph.agui.events import AGUIEvent
 
 
 class AGUIConsoleRenderer:
diff --git a/haiku_rag_slim/haiku/rag/agui/emitter.py b/haiku_rag_slim/haiku/rag/graph/agui/emitter.py
similarity index 99%
rename from haiku_rag_slim/haiku/rag/agui/emitter.py
rename to haiku_rag_slim/haiku/rag/graph/agui/emitter.py
index b634f771..2c284d46 100644
--- a/haiku_rag_slim/haiku/rag/agui/emitter.py
+++ b/haiku_rag_slim/haiku/rag/graph/agui/emitter.py
@@ -7,7 +7,7 @@ from uuid import uuid4
 
 from pydantic import BaseModel
 
-from haiku.rag.agui.events import (
+from haiku.rag.graph.agui.events import (
     AGUIEvent,
     emit_activity,
     emit_run_error,
diff --git a/haiku_rag_slim/haiku/rag/agui/events.py b/haiku_rag_slim/haiku/rag/graph/agui/events.py
similarity index 99%
rename from haiku_rag_slim/haiku/rag/agui/events.py
rename to haiku_rag_slim/haiku/rag/graph/agui/events.py
index d439d005..a7be3d73 100644
--- a/haiku_rag_slim/haiku/rag/agui/events.py
+++ b/haiku_rag_slim/haiku/rag/graph/agui/events.py
@@ -5,7 +5,7 @@ from uuid import uuid4
 
 from pydantic import BaseModel
 
-from haiku.rag.agui.state import compute_state_delta
+from haiku.rag.graph.agui.state import compute_state_delta
 
 # Type aliases for AG-UI events (actual types from ag_ui.core will be used at runtime)
 AGUIEvent = dict[str, Any]
diff --git a/haiku_rag_slim/haiku/rag/agui/server.py b/haiku_rag_slim/haiku/rag/graph/agui/server.py
similarity index 94%
rename from haiku_rag_slim/haiku/rag/agui/server.py
rename to haiku_rag_slim/haiku/rag/graph/agui/server.py
index ff1be032..e7f7a829 100644
--- a/haiku_rag_slim/haiku/rag/agui/server.py
+++ b/haiku_rag_slim/haiku/rag/graph/agui/server.py
@@ -13,9 +13,9 @@ from starlette.requests import Request
 from starlette.responses import JSONResponse, StreamingResponse
 from starlette.routing import Route
 
-from haiku.rag.agui.events import AGUIEvent
-from haiku.rag.agui.stream import stream_graph
 from haiku.rag.config.models import AGUIConfig
+from haiku.rag.graph.agui.events import AGUIEvent
+from haiku.rag.graph.agui.stream import stream_graph
 
 
 class GraphDeps(Protocol):
@@ -157,12 +157,12 @@ def create_agui_server(config: Any, db_path: Any | None = None) -> Starlette:
         Starlette app with research and deep ask endpoints
     """
     from haiku.rag.client import HaikuRAG
-    from haiku.rag.qa.deep.dependencies import DeepQAContext
-    from haiku.rag.qa.deep.graph import build_deep_qa_graph
-    from haiku.rag.qa.deep.state import DeepQADeps, DeepQAState
-    from haiku.rag.research.dependencies import ResearchContext
-    from haiku.rag.research.graph import build_research_graph
-    from haiku.rag.research.state import ResearchDeps, ResearchState
+    from haiku.rag.graph.deep_qa.dependencies import DeepQAContext
+    from haiku.rag.graph.deep_qa.graph import build_deep_qa_graph
+    from haiku.rag.graph.deep_qa.state import DeepQADeps, DeepQAState
+    from haiku.rag.graph.research.dependencies import ResearchContext
+    from haiku.rag.graph.research.graph import build_research_graph
+    from haiku.rag.graph.research.state import ResearchDeps, ResearchState
 
     # Store client reference for proper lifecycle management
     _client_cache: dict[str, HaikuRAG] = {}
diff --git a/haiku_rag_slim/haiku/rag/agui/state.py b/haiku_rag_slim/haiku/rag/graph/agui/state.py
similarity index 100%
rename from haiku_rag_slim/haiku/rag/agui/state.py
rename to haiku_rag_slim/haiku/rag/graph/agui/state.py
diff --git a/haiku_rag_slim/haiku/rag/agui/stream.py b/haiku_rag_slim/haiku/rag/graph/agui/stream.py
similarity index 95%
rename from haiku_rag_slim/haiku/rag/agui/stream.py
rename to haiku_rag_slim/haiku/rag/graph/agui/stream.py
index e91b9b64..75f6a3e5 100644
--- a/haiku_rag_slim/haiku/rag/agui/stream.py
+++ b/haiku_rag_slim/haiku/rag/graph/agui/stream.py
@@ -7,8 +7,8 @@ from typing import Any, Protocol
 
 from pydantic import BaseModel
 
-from haiku.rag.agui.emitter import AGUIEmitter
-from haiku.rag.agui.events import AGUIEvent
+from haiku.rag.graph.agui.emitter import AGUIEmitter
+from haiku.rag.graph.agui.events import AGUIEvent
 
 
 class GraphDeps(Protocol):
diff --git a/haiku_rag_slim/haiku/rag/graph/common/__init__.py b/haiku_rag_slim/haiku/rag/graph/common/__init__.py
new file mode 100644
index 00000000..e2a53f16
--- /dev/null
+++ b/haiku_rag_slim/haiku/rag/graph/common/__init__.py
@@ -0,0 +1,5 @@
+"""Common utilities for graph implementations."""
+
+from haiku.rag.graph.common.utils import get_model
+
+__all__ = ["get_model"]
diff --git a/haiku_rag_slim/haiku/rag/graph_common/models.py b/haiku_rag_slim/haiku/rag/graph/common/models.py
similarity index 100%
rename from haiku_rag_slim/haiku/rag/graph_common/models.py
rename to haiku_rag_slim/haiku/rag/graph/common/models.py
diff --git a/haiku_rag_slim/haiku/rag/graph_common/prompts.py b/haiku_rag_slim/haiku/rag/graph/common/prompts.py
similarity index 100%
rename from haiku_rag_slim/haiku/rag/graph_common/prompts.py
rename to haiku_rag_slim/haiku/rag/graph/common/prompts.py
diff --git a/haiku_rag_slim/haiku/rag/graph_common/utils.py b/haiku_rag_slim/haiku/rag/graph/common/utils.py
similarity index 74%
rename from haiku_rag_slim/haiku/rag/graph_common/utils.py
rename to haiku_rag_slim/haiku/rag/graph/common/utils.py
index f24fb06c..19c424c8 100644
--- a/haiku_rag_slim/haiku/rag/graph_common/utils.py
+++ b/haiku_rag_slim/haiku/rag/graph/common/utils.py
@@ -1,7 +1,5 @@
 """Common utilities for all graph implementations."""
 
-from typing import Any, Protocol
-
 from pydantic_ai.models.openai import OpenAIChatModel
 from pydantic_ai.providers.ollama import OllamaProvider
 from pydantic_ai.providers.openai import OpenAIProvider
@@ -9,12 +7,6 @@ from pydantic_ai.providers.openai import OpenAIProvider
 from haiku.rag.config import Config
 
 
-class HasEmitLog(Protocol):
-    """Protocol for objects that can emit log messages."""
-
-    def emit_log(self, message: str, state: Any = None) -> None: ...
-
-
 def get_model(provider: str, model: str) -> OpenAIChatModel | str:
     """
     Get a model instance for the specified provider and model name.
@@ -50,15 +42,3 @@ def get_model(provider: str, model: str) -> OpenAIChatModel | str:
             f"Unknown model provider: {provider}. "
             f"Supported providers: ollama, vllm, openai, anthropic, gemini, groq, bedrock"
         )
-
-
-def log(deps: HasEmitLog, state: Any, message: str) -> None:
-    """
-    Emit a log message through the dependencies.
-
-    Args:
-        deps: Dependencies object with emit_log method
-        state: Current state (passed to emit_log)
-        message: The message to log
-    """
-    deps.emit_log(message, state)
diff --git a/haiku_rag_slim/haiku/rag/graph/deep_qa/__init__.py b/haiku_rag_slim/haiku/rag/graph/deep_qa/__init__.py
new file mode 100644
index 00000000..aaeb1ae9
--- /dev/null
+++ b/haiku_rag_slim/haiku/rag/graph/deep_qa/__init__.py
@@ -0,0 +1 @@
+from haiku.rag.graph.deep_qa.models import DeepQAAnswer
diff --git a/haiku_rag_slim/haiku/rag/qa/deep/dependencies.py b/haiku_rag_slim/haiku/rag/graph/deep_qa/dependencies.py
similarity index 87%
rename from haiku_rag_slim/haiku/rag/qa/deep/dependencies.py
rename to haiku_rag_slim/haiku/rag/graph/deep_qa/dependencies.py
index f8bce190..1c33262b 100644
--- a/haiku_rag_slim/haiku/rag/qa/deep/dependencies.py
+++ b/haiku_rag_slim/haiku/rag/graph/deep_qa/dependencies.py
@@ -1,8 +1,7 @@
 from pydantic import BaseModel, Field
-from rich.console import Console
 
 from haiku.rag.client import HaikuRAG
-from haiku.rag.graph_common.models import SearchAnswer
+from haiku.rag.graph.common.models import SearchAnswer
 
 
 class DeepQAContext(BaseModel):
@@ -26,4 +25,3 @@ class DeepQADependencies(BaseModel):
 
     client: HaikuRAG = Field(description="RAG client for document operations")
     context: DeepQAContext = Field(description="Shared QA context")
-    console: Console | None = None
diff --git a/haiku_rag_slim/haiku/rag/qa/deep/graph.py b/haiku_rag_slim/haiku/rag/graph/deep_qa/graph.py
similarity index 95%
rename from haiku_rag_slim/haiku/rag/qa/deep/graph.py
rename to haiku_rag_slim/haiku/rag/graph/deep_qa/graph.py
index 4ae92bc3..61f2a121 100644
--- a/haiku_rag_slim/haiku/rag/qa/deep/graph.py
+++ b/haiku_rag_slim/haiku/rag/graph/deep_qa/graph.py
@@ -8,17 +8,17 @@ from pydantic_graph.beta.join import reduce_list_append
 
 from haiku.rag.config import Config
 from haiku.rag.config.models import AppConfig
-from haiku.rag.graph_common import get_model
-from haiku.rag.graph_common.models import ResearchPlan, SearchAnswer
-from haiku.rag.graph_common.prompts import PLAN_PROMPT, SEARCH_AGENT_PROMPT
-from haiku.rag.qa.deep.dependencies import DeepQADependencies
-from haiku.rag.qa.deep.models import DeepQAAnswer, DeepQAEvaluation
-from haiku.rag.qa.deep.prompts import (
+from haiku.rag.graph.common import get_model
+from haiku.rag.graph.common.models import ResearchPlan, SearchAnswer
+from haiku.rag.graph.common.prompts import PLAN_PROMPT, SEARCH_AGENT_PROMPT
+from haiku.rag.graph.deep_qa.dependencies import DeepQADependencies
+from haiku.rag.graph.deep_qa.models import DeepQAAnswer, DeepQAEvaluation
+from haiku.rag.graph.deep_qa.prompts import (
     DECISION_PROMPT,
     SYNTHESIS_PROMPT,
     SYNTHESIS_PROMPT_WITH_CITATIONS,
 )
-from haiku.rag.qa.deep.state import DeepQADeps, DeepQAState
+from haiku.rag.graph.deep_qa.state import DeepQADeps, DeepQAState
 
 
 def build_deep_qa_graph(
@@ -77,7 +77,6 @@ def build_deep_qa_graph(
             agent_deps = DeepQADependencies(
                 client=deps.client,
                 context=state.context,
-                console=None,
             )
             plan_result = await plan_agent.run(prompt, deps=agent_deps)
             state.context.sub_questions = list(plan_result.output.sub_questions)
@@ -151,7 +150,6 @@ def build_deep_qa_graph(
         agent_deps = DeepQADependencies(
             client=deps.client,
             context=state.context,
-            console=None,
         )
         try:
             result = await agent.run(sub_q, deps=agent_deps)
@@ -228,7 +226,6 @@ def build_deep_qa_graph(
             agent_deps = DeepQADependencies(
                 client=deps.client,
                 context=state.context,
-                console=None,
             )
             result = await agent.run(prompt, deps=agent_deps)
             evaluation = result.output
@@ -302,7 +299,6 @@ def build_deep_qa_graph(
             agent_deps = DeepQADependencies(
                 client=deps.client,
                 context=state.context,
-                console=None,
             )
             result = await agent.run(prompt, deps=agent_deps)
 
diff --git a/haiku_rag_slim/haiku/rag/qa/deep/models.py b/haiku_rag_slim/haiku/rag/graph/deep_qa/models.py
similarity index 100%
rename from haiku_rag_slim/haiku/rag/qa/deep/models.py
rename to haiku_rag_slim/haiku/rag/graph/deep_qa/models.py
diff --git a/haiku_rag_slim/haiku/rag/qa/deep/prompts.py b/haiku_rag_slim/haiku/rag/graph/deep_qa/prompts.py
similarity index 100%
rename from haiku_rag_slim/haiku/rag/qa/deep/prompts.py
rename to haiku_rag_slim/haiku/rag/graph/deep_qa/prompts.py
diff --git a/haiku_rag_slim/haiku/rag/qa/deep/state.py b/haiku_rag_slim/haiku/rag/graph/deep_qa/state.py
similarity index 96%
rename from haiku_rag_slim/haiku/rag/qa/deep/state.py
rename to haiku_rag_slim/haiku/rag/graph/deep_qa/state.py
index a340d42d..179542a6 100644
--- a/haiku_rag_slim/haiku/rag/qa/deep/state.py
+++ b/haiku_rag_slim/haiku/rag/graph/deep_qa/state.py
@@ -5,7 +5,7 @@ from typing import TYPE_CHECKING, Any
 from pydantic import BaseModel, Field
 
 from haiku.rag.client import HaikuRAG
-from haiku.rag.qa.deep.dependencies import DeepQAContext
+from haiku.rag.graph.deep_qa.dependencies import DeepQAContext
 
 if TYPE_CHECKING:
     from haiku.rag.config.models import AppConfig
diff --git a/haiku_rag_slim/haiku/rag/graph/research/__init__.py b/haiku_rag_slim/haiku/rag/graph/research/__init__.py
new file mode 100644
index 00000000..60f53a90
--- /dev/null
+++ b/haiku_rag_slim/haiku/rag/graph/research/__init__.py
@@ -0,0 +1,3 @@
+from haiku.rag.graph.common.models import SearchAnswer
+from haiku.rag.graph.research.dependencies import ResearchContext, ResearchDependencies
+from haiku.rag.graph.research.models import EvaluationResult, ResearchReport
diff --git a/haiku_rag_slim/haiku/rag/research/common.py b/haiku_rag_slim/haiku/rag/graph/research/common.py
similarity index 95%
rename from haiku_rag_slim/haiku/rag/research/common.py
rename to haiku_rag_slim/haiku/rag/graph/research/common.py
index bd6e349d..28c1aada 100644
--- a/haiku_rag_slim/haiku/rag/research/common.py
+++ b/haiku_rag_slim/haiku/rag/graph/research/common.py
@@ -1,7 +1,7 @@
 from pydantic_ai import format_as_xml
 
-from haiku.rag.research.dependencies import ResearchContext
-from haiku.rag.research.models import InsightAnalysis
+from haiku.rag.graph.research.dependencies import ResearchContext
+from haiku.rag.graph.research.models import InsightAnalysis
 
 
 def format_context_for_prompt(context: ResearchContext) -> str:
diff --git a/haiku_rag_slim/haiku/rag/research/dependencies.py b/haiku_rag_slim/haiku/rag/graph/research/dependencies.py
similarity index 98%
rename from haiku_rag_slim/haiku/rag/research/dependencies.py
rename to haiku_rag_slim/haiku/rag/graph/research/dependencies.py
index 39bf641c..fe65cc03 100644
--- a/haiku_rag_slim/haiku/rag/research/dependencies.py
+++ b/haiku_rag_slim/haiku/rag/graph/research/dependencies.py
@@ -3,8 +3,8 @@ from collections.abc import Iterable
 from pydantic import BaseModel, Field
 
 from haiku.rag.client import HaikuRAG
-from haiku.rag.graph_common.models import SearchAnswer
-from haiku.rag.research.models import (
+from haiku.rag.graph.common.models import SearchAnswer
+from haiku.rag.graph.research.models import (
     GapRecord,
     InsightAnalysis,
     InsightRecord,
diff --git a/haiku_rag_slim/haiku/rag/research/graph.py b/haiku_rag_slim/haiku/rag/graph/research/graph.py
similarity index 96%
rename from haiku_rag_slim/haiku/rag/research/graph.py
rename to haiku_rag_slim/haiku/rag/graph/research/graph.py
index b2019e00..227a33af 100644
--- a/haiku_rag_slim/haiku/rag/research/graph.py
+++ b/haiku_rag_slim/haiku/rag/graph/research/graph.py
@@ -8,25 +8,25 @@ from pydantic_graph.beta.join import reduce_list_append
 
 from haiku.rag.config import Config
 from haiku.rag.config.models import AppConfig
-from haiku.rag.graph_common import get_model
-from haiku.rag.graph_common.models import ResearchPlan, SearchAnswer
-from haiku.rag.graph_common.prompts import PLAN_PROMPT, SEARCH_AGENT_PROMPT
-from haiku.rag.research.common import (
+from haiku.rag.graph.common import get_model
+from haiku.rag.graph.common.models import ResearchPlan, SearchAnswer
+from haiku.rag.graph.common.prompts import PLAN_PROMPT, SEARCH_AGENT_PROMPT
+from haiku.rag.graph.research.common import (
     format_analysis_for_prompt,
     format_context_for_prompt,
 )
-from haiku.rag.research.dependencies import ResearchDependencies
-from haiku.rag.research.models import (
+from haiku.rag.graph.research.dependencies import ResearchDependencies
+from haiku.rag.graph.research.models import (
     EvaluationResult,
     InsightAnalysis,
     ResearchReport,
 )
-from haiku.rag.research.prompts import (
+from haiku.rag.graph.research.prompts import (
     DECISION_AGENT_PROMPT,
     INSIGHT_AGENT_PROMPT,
     SYNTHESIS_AGENT_PROMPT,
 )
-from haiku.rag.research.state import ResearchDeps, ResearchState
+from haiku.rag.graph.research.state import ResearchDeps, ResearchState
 
 
 def build_research_graph(
diff --git a/haiku_rag_slim/haiku/rag/research/models.py b/haiku_rag_slim/haiku/rag/graph/research/models.py
similarity index 100%
rename from haiku_rag_slim/haiku/rag/research/models.py
rename to haiku_rag_slim/haiku/rag/graph/research/models.py
diff --git a/haiku_rag_slim/haiku/rag/research/prompts.py b/haiku_rag_slim/haiku/rag/graph/research/prompts.py
similarity index 100%
rename from haiku_rag_slim/haiku/rag/research/prompts.py
rename to haiku_rag_slim/haiku/rag/graph/research/prompts.py
diff --git a/haiku_rag_slim/haiku/rag/research/state.py b/haiku_rag_slim/haiku/rag/graph/research/state.py
similarity index 91%
rename from haiku_rag_slim/haiku/rag/research/state.py
rename to haiku_rag_slim/haiku/rag/graph/research/state.py
index 72e341f5..8ac49c95 100644
--- a/haiku_rag_slim/haiku/rag/research/state.py
+++ b/haiku_rag_slim/haiku/rag/graph/research/state.py
@@ -5,12 +5,16 @@ from typing import TYPE_CHECKING
 from pydantic import BaseModel, Field
 
 from haiku.rag.client import HaikuRAG
-from haiku.rag.research.dependencies import ResearchContext
-from haiku.rag.research.models import EvaluationResult, InsightAnalysis, ResearchReport
+from haiku.rag.graph.research.dependencies import ResearchContext
+from haiku.rag.graph.research.models import (
+    EvaluationResult,
+    InsightAnalysis,
+    ResearchReport,
+)
 
 if TYPE_CHECKING:
-    from haiku.rag.agui.emitter import AGUIEmitter
     from haiku.rag.config.models import AppConfig
+    from haiku.rag.graph.agui.emitter import AGUIEmitter
 
 
 @dataclass
diff --git a/haiku_rag_slim/haiku/rag/graph_common/__init__.py b/haiku_rag_slim/haiku/rag/graph_common/__init__.py
deleted file mode 100644
index dc47bee0..00000000
--- a/haiku_rag_slim/haiku/rag/graph_common/__init__.py
+++ /dev/null
@@ -1,5 +0,0 @@
-"""Common utilities for graph implementations."""
-
-from haiku.rag.graph_common.utils import get_model, log
-
-__all__ = ["get_model", "log"]
diff --git a/haiku_rag_slim/haiku/rag/mcp.py b/haiku_rag_slim/haiku/rag/mcp.py
index 25cd2fec..c6c3f97e 100644
--- a/haiku_rag_slim/haiku/rag/mcp.py
+++ b/haiku_rag_slim/haiku/rag/mcp.py
@@ -6,7 +6,7 @@ from pydantic import BaseModel
 
 from haiku.rag.client import HaikuRAG
 from haiku.rag.config import AppConfig, Config
-from haiku.rag.research.models import ResearchReport
+from haiku.rag.graph.research.models import ResearchReport
 
 
 class SearchResult(BaseModel):
@@ -191,9 +191,9 @@ def create_mcp_server(db_path: Path, config: AppConfig = Config) -> FastMCP:
         try:
             async with HaikuRAG(db_path, config=config) as rag:
                 if deep:
-                    from haiku.rag.qa.deep.dependencies import DeepQAContext
-                    from haiku.rag.qa.deep.graph import build_deep_qa_graph
-                    from haiku.rag.qa.deep.state import DeepQADeps, DeepQAState
+                    from haiku.rag.graph.deep_qa.dependencies import DeepQAContext
+                    from haiku.rag.graph.deep_qa.graph import build_deep_qa_graph
+                    from haiku.rag.graph.deep_qa.state import DeepQADeps, DeepQAState
 
                     graph = build_deep_qa_graph(config=config)
                     context = DeepQAContext(
@@ -226,9 +226,9 @@ def create_mcp_server(db_path: Path, config: AppConfig = Config) -> FastMCP:
             A research report with findings, or None if an error occurred.
         """
         try:
-            from haiku.rag.research.dependencies import ResearchContext
-            from haiku.rag.research.graph import build_research_graph
-            from haiku.rag.research.state import ResearchDeps, ResearchState
+            from haiku.rag.graph.research.dependencies import ResearchContext
+            from haiku.rag.graph.research.graph import build_research_graph
+            from haiku.rag.graph.research.state import ResearchDeps, ResearchState
 
             async with HaikuRAG(db_path, config=config) as rag:
                 graph = build_research_graph(config=config)
diff --git a/haiku_rag_slim/haiku/rag/qa/deep/__init__.py b/haiku_rag_slim/haiku/rag/qa/deep/__init__.py
deleted file mode 100644
index 0dc102f6..00000000
--- a/haiku_rag_slim/haiku/rag/qa/deep/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-from haiku.rag.qa.deep.models import DeepQAAnswer
diff --git a/haiku_rag_slim/haiku/rag/research/__init__.py b/haiku_rag_slim/haiku/rag/research/__init__.py
deleted file mode 100644
index 9406a89c..00000000
--- a/haiku_rag_slim/haiku/rag/research/__init__.py
+++ /dev/null
@@ -1,3 +0,0 @@
-from haiku.rag.graph_common.models import SearchAnswer
-from haiku.rag.research.dependencies import ResearchContext, ResearchDependencies
-from haiku.rag.research.models import EvaluationResult, ResearchReport
diff --git a/tests/graph/__init__.py b/tests/graph/__init__.py
new file mode 100644
index 00000000..8a28b35f
--- /dev/null
+++ b/tests/graph/__init__.py
@@ -0,0 +1 @@
+"""Tests for haiku.rag.graph module."""
diff --git a/tests/agui/__init__.py b/tests/graph/agui/__init__.py
similarity index 100%
rename from tests/agui/__init__.py
rename to tests/graph/agui/__init__.py
diff --git a/tests/agui/test_cli_renderer.py b/tests/graph/agui/test_cli_renderer.py
similarity index 97%
rename from tests/agui/test_cli_renderer.py
rename to tests/graph/agui/test_cli_renderer.py
index c01d6934..738b0bcc 100644
--- a/tests/agui/test_cli_renderer.py
+++ b/tests/graph/agui/test_cli_renderer.py
@@ -4,8 +4,8 @@ import pytest
 from pydantic import BaseModel
 from rich.console import Console
 
-from haiku.rag.agui.cli_renderer import AGUIConsoleRenderer
-from haiku.rag.agui.events import (
+from haiku.rag.graph.agui.cli_renderer import AGUIConsoleRenderer
+from haiku.rag.graph.agui.events import (
     emit_activity,
     emit_run_error,
     emit_run_finished,
diff --git a/tests/agui/test_emitter.py b/tests/graph/agui/test_emitter.py
similarity index 99%
rename from tests/agui/test_emitter.py
rename to tests/graph/agui/test_emitter.py
index 5a057247..5e6148d1 100644
--- a/tests/agui/test_emitter.py
+++ b/tests/graph/agui/test_emitter.py
@@ -5,7 +5,7 @@ import asyncio
 import pytest
 from pydantic import BaseModel
 
-from haiku.rag.agui.emitter import AGUIEmitter
+from haiku.rag.graph.agui.emitter import AGUIEmitter
 
 
 class TestState(BaseModel):
diff --git a/tests/agui/test_events.py b/tests/graph/agui/test_events.py
similarity index 99%
rename from tests/agui/test_events.py
rename to tests/graph/agui/test_events.py
index 67db2e22..e400f99d 100644
--- a/tests/agui/test_events.py
+++ b/tests/graph/agui/test_events.py
@@ -2,7 +2,7 @@
 
 from pydantic import BaseModel
 
-from haiku.rag.agui.events import (
+from haiku.rag.graph.agui.events import (
     emit_activity,
     emit_run_error,
     emit_run_finished,
diff --git a/tests/agui/test_server.py b/tests/graph/agui/test_server.py
similarity index 98%
rename from tests/agui/test_server.py
rename to tests/graph/agui/test_server.py
index 2752b153..a145f7f6 100644
--- a/tests/agui/test_server.py
+++ b/tests/graph/agui/test_server.py
@@ -4,8 +4,8 @@ import pytest
 from pydantic import BaseModel
 from starlette.testclient import TestClient
 
-from haiku.rag.agui.server import RunAgentInput, create_agui_app, format_sse_event
 from haiku.rag.config.models import AGUIConfig
+from haiku.rag.graph.agui.server import RunAgentInput, create_agui_app, format_sse_event
 
 
 class SimpleState(BaseModel):
diff --git a/tests/agui/test_stream.py b/tests/graph/agui/test_stream.py
similarity index 98%
rename from tests/agui/test_stream.py
rename to tests/graph/agui/test_stream.py
index 1aca01b4..daa428b0 100644
--- a/tests/agui/test_stream.py
+++ b/tests/graph/agui/test_stream.py
@@ -5,8 +5,8 @@ from dataclasses import dataclass
 import pytest
 from pydantic import BaseModel
 
-from haiku.rag.agui.emitter import AGUIEmitter
-from haiku.rag.agui.stream import stream_graph
+from haiku.rag.graph.agui.emitter import AGUIEmitter
+from haiku.rag.graph.agui.stream import stream_graph
 
 
 class TestState(BaseModel):
diff --git a/tests/test_deep_qa.py b/tests/graph/test_deep_qa.py
similarity index 83%
rename from tests/test_deep_qa.py
rename to tests/graph/test_deep_qa.py
index b6757498..582b3242 100644
--- a/tests/test_deep_qa.py
+++ b/tests/graph/test_deep_qa.py
@@ -2,10 +2,10 @@ import pytest
 from pydantic_ai.models.test import TestModel
 
 from haiku.rag.client import HaikuRAG
-from haiku.rag.graph_common.models import SearchAnswer
-from haiku.rag.qa.deep.dependencies import DeepQAContext
-from haiku.rag.qa.deep.graph import build_deep_qa_graph
-from haiku.rag.qa.deep.state import DeepQADeps, DeepQAState
+from haiku.rag.graph.common.models import SearchAnswer
+from haiku.rag.graph.deep_qa.dependencies import DeepQAContext
+from haiku.rag.graph.deep_qa.graph import build_deep_qa_graph
+from haiku.rag.graph.deep_qa.state import DeepQADeps, DeepQAState
 
 
 @pytest.mark.asyncio
@@ -16,8 +16,8 @@ async def test_deep_qa_graph_end_to_end(monkeypatch, temp_db_path):
     def test_model_factory(provider, model):
         return TestModel()
 
-    monkeypatch.setattr("haiku.rag.graph_common.utils.get_model", test_model_factory)
-    monkeypatch.setattr("haiku.rag.qa.deep.graph.get_model", test_model_factory)
+    monkeypatch.setattr("haiku.rag.graph.common.utils.get_model", test_model_factory)
+    monkeypatch.setattr("haiku.rag.graph.deep_qa.graph.get_model", test_model_factory)
 
     graph = build_deep_qa_graph()
 
@@ -50,8 +50,8 @@ async def test_deep_qa_with_citations(monkeypatch, temp_db_path):
     def test_model_factory(provider, model):
         return TestModel()
 
-    monkeypatch.setattr("haiku.rag.graph_common.utils.get_model", test_model_factory)
-    monkeypatch.setattr("haiku.rag.qa.deep.graph.get_model", test_model_factory)
+    monkeypatch.setattr("haiku.rag.graph.common.utils.get_model", test_model_factory)
+    monkeypatch.setattr("haiku.rag.graph.deep_qa.graph.get_model", test_model_factory)
 
     graph = build_deep_qa_graph()
 
diff --git a/tests/test_research_graph.py b/tests/graph/test_research_graph.py
similarity index 85%
rename from tests/test_research_graph.py
rename to tests/graph/test_research_graph.py
index 94f1f6a3..f452b022 100644
--- a/tests/test_research_graph.py
+++ b/tests/graph/test_research_graph.py
@@ -3,11 +3,11 @@ import asyncio
 import pytest
 from pydantic_ai.models.test import TestModel
 
-from haiku.rag.agui.stream import stream_graph
 from haiku.rag.client import HaikuRAG
-from haiku.rag.research.dependencies import ResearchContext
-from haiku.rag.research.graph import build_research_graph
-from haiku.rag.research.state import ResearchDeps, ResearchState
+from haiku.rag.graph.agui.stream import stream_graph
+from haiku.rag.graph.research.dependencies import ResearchContext
+from haiku.rag.graph.research.graph import build_research_graph
+from haiku.rag.graph.research.state import ResearchDeps, ResearchState
 
 
 def test_build_graph_and_state():
@@ -39,8 +39,8 @@ async def test_graph_end_to_end_with_test_model(monkeypatch, temp_db_path):
     def test_model_factory(_provider, _model):
         return TestModel()
 
-    monkeypatch.setattr("haiku.rag.graph_common.utils.get_model", test_model_factory)
-    monkeypatch.setattr("haiku.rag.research.graph.get_model", test_model_factory)
+    monkeypatch.setattr("haiku.rag.graph.common.utils.get_model", test_model_factory)
+    monkeypatch.setattr("haiku.rag.graph.research.graph.get_model", test_model_factory)
 
     graph = build_research_graph()
 
diff --git a/tests/test_app.py b/tests/test_app.py
index 51153aa4..e189c022 100644
--- a/tests/test_app.py
+++ b/tests/test_app.py
@@ -343,7 +343,7 @@ async def test_ask_with_verbose(app: HaikuRAGApp, monkeypatch):
 @pytest.mark.asyncio
 async def test_ask_with_deep(app: HaikuRAGApp, monkeypatch):
     """Test asking a question with deep QA."""
-    from haiku.rag.qa.deep.models import DeepQAAnswer
+    from haiku.rag.graph.deep_qa.models import DeepQAAnswer
 
     mock_output = DeepQAAnswer(answer="Deep QA answer", sources=["test.md"])
 
@@ -358,7 +358,7 @@ async def test_ask_with_deep(app: HaikuRAGApp, monkeypatch):
 
     with patch("haiku.rag.app.HaikuRAG", return_value=mock_client):
         with patch(
-            "haiku.rag.qa.deep.graph.build_deep_qa_graph", return_value=mock_graph
+            "haiku.rag.graph.deep_qa.graph.build_deep_qa_graph", return_value=mock_graph
         ):
             await app.ask("test question", deep=True)
 
@@ -371,7 +371,7 @@ async def test_ask_with_deep(app: HaikuRAGApp, monkeypatch):
 @pytest.mark.asyncio
 async def test_ask_with_deep_and_cite(app: HaikuRAGApp, monkeypatch):
     """Test asking a question with deep QA and citations."""
-    from haiku.rag.qa.deep.models import DeepQAAnswer
+    from haiku.rag.graph.deep_qa.models import DeepQAAnswer
 
     mock_output = DeepQAAnswer(
         answer="Deep QA answer with citations [test.md]", sources=["test.md"]
@@ -388,7 +388,7 @@ async def test_ask_with_deep_and_cite(app: HaikuRAGApp, monkeypatch):
 
     with patch("haiku.rag.app.HaikuRAG", return_value=mock_client):
         with patch(
-            "haiku.rag.qa.deep.graph.build_deep_qa_graph", return_value=mock_graph
+            "haiku.rag.graph.deep_qa.graph.build_deep_qa_graph", return_value=mock_graph
         ):
             await app.ask("test question", deep=True, cite=True)
 
@@ -417,10 +417,10 @@ async def test_ask_with_deep_and_verbose(app: HaikuRAGApp, monkeypatch):
 
     with patch("haiku.rag.app.HaikuRAG", return_value=mock_client):
         with patch(
-            "haiku.rag.qa.deep.graph.build_deep_qa_graph", return_value=mock_graph
+            "haiku.rag.graph.deep_qa.graph.build_deep_qa_graph", return_value=mock_graph
         ):
             with patch(
-                "haiku.rag.agui.AGUIConsoleRenderer", return_value=mock_renderer
+                "haiku.rag.graph.agui.AGUIConsoleRenderer", return_value=mock_renderer
             ):
                 await app.ask("test question", deep=True, verbose=True)
 
diff --git a/tests/test_mcp.py b/tests/test_mcp.py
index de2956d3..389f11bc 100644
--- a/tests/test_mcp.py
+++ b/tests/test_mcp.py
@@ -4,8 +4,8 @@ from unittest.mock import AsyncMock, patch
 
 import pytest
 
+from haiku.rag.graph.research.models import ResearchReport
 from haiku.rag.mcp import create_mcp_server
-from haiku.rag.research.models import ResearchReport
 from haiku.rag.store.models.document import Document
 
 
@@ -249,7 +249,9 @@ async def test_mcp_ask_question_deep():
 
         with (
             patch("haiku.rag.mcp.HaikuRAG") as mock_rag_class,
-            patch("haiku.rag.qa.deep.graph.build_deep_qa_graph") as mock_graph_builder,
+            patch(
+                "haiku.rag.graph.deep_qa.graph.build_deep_qa_graph"
+            ) as mock_graph_builder,
         ):
             mock_rag = AsyncMock()
             mock_rag_class.return_value.__aenter__ = AsyncMock(return_value=mock_rag)
@@ -291,7 +293,7 @@ async def test_mcp_research_question():
         with (
             patch("haiku.rag.mcp.HaikuRAG") as mock_rag_class,
             patch(
-                "haiku.rag.research.graph.build_research_graph"
+                "haiku.rag.graph.research.graph.build_research_graph"
             ) as mock_graph_builder,
         ):
             mock_rag = AsyncMock()