refactor(layout): phase2 rewrite call sites to new paths, remove shims

coding-agent/src/coding_agent/action_safety/validation_feedback.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 import hashlib
-from coding_agent.context_pack import (
+from coding_agent.topics.context_pack import (
     ContextPack,
     ContextPackItem,
     ContextPackRenderer,

coding-agent/src/coding_agent/approval/interactions.py

@@ -7,7 +7,7 @@
 from math import isfinite
 from typing import Protocol, cast
 
-from coding_agent.runtime_store import (
+from coding_agent.stores.runtime_store import (
     AgentInteractionRecord,
     JSONObject,
     JSONValue,

coding-agent/src/coding_agent/bee/launch.py

@@ -32,9 +32,9 @@
     write_bee_workspace_run_artifacts,
 )
 from coding_agent.observability import record_bee_launch_metric
-from coding_agent.scheduled_runs import ScheduledLaunchIntent, ScheduleTriggerRecord
-from coding_agent.topic_lifecycle import TopicLifecycle
-from coding_agent.topic_store import JSONObject, JSONValue, TopicRecord
+from coding_agent.runs.scheduled import ScheduledLaunchIntent, ScheduleTriggerRecord
+from coding_agent.topics.lifecycle import TopicLifecycle
+from coding_agent.topics.store import JSONObject, JSONValue, TopicRecord
 
 BeeLaunchSource = str
 BeeLaunchStatus = str

coding-agent/src/coding_agent/bee/runtime.py

@@ -15,7 +15,7 @@
 from agentkit.storage.pg import AsyncPGPool, PGPool
 from agentkit.tape.anchor import Anchor
 from agentkit.tape.tape import Tape
-from coding_agent.topic_store import (
+from coding_agent.topics.store import (
     JSONObject,
     JSONValue,
     TopicAnchorRecord,

coding-agent/src/coding_agent/bee/template_pack.py

@@ -26,7 +26,7 @@
     load_bee_workspace_command_intents,
     load_bee_workspace_template,
 )
-from coding_agent.topic_store import JSONObject
+from coding_agent.topics.store import JSONObject
 
 _MANIFEST_CANDIDATES: Final[tuple[tuple[str, str], ...]] = (
     ("bee-pack.yaml", "yaml"),

coding-agent/src/coding_agent/bee/workspace.py

@@ -15,7 +15,7 @@
 import yaml
 
 from coding_agent.bee.runtime import BeeTaskManifest, parse_bee_task_manifest
-from coding_agent.topic_store import JSONObject
+from coding_agent.topics.store import JSONObject
 
 _BEE_DIR: Final[str] = ".bee"
 _TEMPLATES_DIR: Final[str] = "templates"

coding-agent/src/coding_agent/cli/acp_command.py

@@ -11,7 +11,7 @@
 from coding_agent.acp import AcpServer, AcpMode, run_stdio
 from coding_agent.approval import ApprovalPolicy
 from coding_agent.cli.local_runtime import create_local_cli_session_manager
-from coding_agent.local_storage import (
+from coding_agent.stores.local import (
     local_data_dir,
     local_sqlite_path,
     local_sqlite_storage_config,

coding-agent/src/coding_agent/cli/local_runtime.py

@@ -12,8 +12,8 @@
 from coding_agent.adapter import PipelineAdapter
 from coding_agent.core.config import Config
 from coding_agent.runs import UNSET, UnsetType
-from coding_agent.local_storage import local_sqlite_storage_config
-from coding_agent.local_storage import local_sqlite_path_from_storage_config
+from coding_agent.stores.local import local_sqlite_storage_config
+from coding_agent.stores.local import local_sqlite_path_from_storage_config
 from coding_agent.server.session_manager import SessionManager
 from coding_agent.server.stores.session_owner_store import SQLiteSessionOwnerStore
 
@@ -360,7 +360,7 @@ def create_local_cli_session_manager(
 
 
 def create_agent(*args: Any, **kwargs: Any) -> tuple[Any, Any]:
-    return importlib.import_module("coding_agent.app").create_agent(*args, **kwargs)
+    return importlib.import_module("coding_agent.core.app").create_agent(*args, **kwargs)
 
 
 def create_local_cli_runtime(config: Config, consumer: Any) -> LocalCliRuntime:

coding-agent/src/coding_agent/cli/main.py

@@ -13,7 +13,7 @@
 
 import click
 
-from coding_agent.app import create_agent, create_child_pipeline  # noqa: F401
+from coding_agent.core.app import create_agent, create_child_pipeline  # noqa: F401
 from coding_agent.cli.acp_command import acp
 from coding_agent.cli.kb_commands import kb
 from coding_agent.cli.oauth_commands import oauth_cli
@@ -30,8 +30,8 @@
     create_local_cli_session_manager,
     local_cli_session_origin,
 )
-from coding_agent.storage_migration import migrate_legacy_storage_to_sqlite
-from coding_agent.local_storage import local_sqlite_storage_config
+from coding_agent.stores.migration import migrate_legacy_storage_to_sqlite
+from coding_agent.stores.local import local_sqlite_storage_config
 from coding_agent.ui.headless import HeadlessConsumer
 from coding_agent.ui.rich_tui import CodingAgentTUI
 from coding_agent.wire.protocol import TurnEnd, WireMessage

coding-agent/src/coding_agent/cli/remote_commands.py

@@ -201,7 +201,7 @@ def _remote_run_once(
         get_remote,
         stream_prompt,
     )
-    from coding_agent.workspace_archive import (
+    from coding_agent.environment.archive import (
         create_workspace_archive_base64,
     )
 
@@ -1528,7 +1528,7 @@ def _download_and_restore_workspace(
         download_workspace_archive,
         download_workspace_manifest,
     )
-    from coding_agent.workspace_archive import extract_workspace_archive_base64
+    from coding_agent.environment.archive import extract_workspace_archive_base64
 
     manifest = download_workspace_manifest(
         base_url=base_url,

coding-agent/src/coding_agent/cli/stats_command.py

@@ -10,7 +10,7 @@
 @click.option("--session", "-s", help="Session ID (default: last)")
 def stats(session: str | None):
     """Show session statistics."""
-    from coding_agent.metrics import collector
+    from coding_agent.observability.metrics import collector
 
     if not session:
         # Use last session

coding-agent/src/coding_agent/core/app.py

@@ -37,7 +37,7 @@
 from coding_agent.plugins.storage import StoragePlugin
 from coding_agent.plugins.summarizer import SummarizerPlugin
 from coding_agent.subagents.coordinator import ChildWorkerCoordinator
-from coding_agent.topic_memory import MemoryReviewStore
+from coding_agent.topics.memory import MemoryReviewStore
 from coding_agent.tools.web_search import create_web_search_backend
 
 ToolFilter = Any

coding-agent/src/coding_agent/events/display.py

@@ -7,7 +7,7 @@
 import uuid
 from typing import Literal, cast
 
-from coding_agent.runtime_store import JSONObject, JSONValue, RuntimeEventRecord
+from coding_agent.stores.runtime_store import JSONObject, JSONValue, RuntimeEventRecord
 
 DisplayEventKind = Literal[
     "assistant_text_delta",

coding-agent/src/coding_agent/events/replay.py

@@ -2,7 +2,7 @@
 
 from dataclasses import dataclass
 
-from coding_agent.runtime_store import RuntimeEventRecord
+from coding_agent.stores.runtime_store import RuntimeEventRecord
 from coding_agent.stores import RuntimeEventStore
 
 from .display import DisplayEvent, project_runtime_events_to_display

coding-agent/src/coding_agent/executors/external.py

@@ -18,12 +18,12 @@
 from agentkit.storage.pg import AsyncPGPool, PGPool
 from coding_agent.action_safety.approval_routing import ActionApprovalRoute
 from coding_agent.action_safety.command_policy import CommandPolicyDecision
-from coding_agent.bee_command_bridge import (
+from coding_agent.bee.command_bridge import (
     BeeCommandIntentPlan,
     BeeNodeCompletionEvidence,
     is_authorized_bee_command_plan,
 )
-from coding_agent.topic_store import JSONObject, JSONValue
+from coding_agent.topics.store import JSONObject, JSONValue
 
 ExecutorKind = str
 ExecutorRunStatus = str

coding-agent/src/coding_agent/plugins/kb.py

@@ -9,7 +9,7 @@
 from agentkit.observability import ObservationSink, record_span
 from agentkit.tape.tape import Tape
 
-from coding_agent.context_pack import (
+from coding_agent.topics.context_pack import (
     ContextPack,
     ContextPackItem,
     ContextPackRenderer,

coding-agent/src/coding_agent/plugins/memory.py

@@ -23,7 +23,7 @@
 from agentkit.directive.types import MemoryRecord
 from agentkit.tape.models import Entry
 from agentkit.tape.tape import Tape
-from coding_agent.context_pack import (
+from coding_agent.topics.context_pack import (
     ContextPack,
     ContextPackItem,
     ContextPackRenderer,

coding-agent/src/coding_agent/plugins/metrics.py

@@ -6,7 +6,7 @@
 from collections import defaultdict
 from typing import Any, Callable
 
-from coding_agent.agent_identity import effective_agent_id, legacy_agent_id_str
+from coding_agent.core.agent_identity import effective_agent_id, legacy_agent_id_str
 
 
 class SessionMetricsPlugin:

coding-agent/src/coding_agent/plugins/storage.py

@@ -19,7 +19,7 @@
 from agentkit.storage.session import FileSessionStore
 from agentkit.storage.sqlite import SQLiteTapeStore
 from agentkit.tape.store import ForkTapeStore
-from coding_agent.local_storage import local_sqlite_path_from_storage_config
+from coding_agent.stores.local import local_sqlite_path_from_storage_config
 
 
 def _load_pg_types() -> tuple[Any, Any, Any, Any]:

coding-agent/src/coding_agent/remote/worker.py

@@ -15,8 +15,8 @@
 
 from agentkit.observability import ObservationSink, record_span
 from coding_agent.adapter import PipelineAdapter
-from coding_agent.app import create_agent
-from coding_agent.adapter_types import TurnOutcome
+from coding_agent.core.app import create_agent
+from coding_agent.adapter.types import TurnOutcome
 from coding_agent.ui.headless import HeadlessConsumer
 from coding_agent.wire.protocol import (
     ApprovalRequest,

coding-agent/src/coding_agent/runs/attached_executor.py

@@ -8,7 +8,7 @@
 from datetime import UTC, datetime, timedelta
 from typing import Any, AsyncContextManager, Protocol, cast
 
-from coding_agent.runtime_store import AgentRunRecord, JSONObject, RuntimeEventRecord
+from coding_agent.stores.runtime_store import AgentRunRecord, JSONObject, RuntimeEventRecord
 from coding_agent.stores import RuntimeRunStore
 
 from .lifecycle import RuntimeRunResumeContext

coding-agent/src/coding_agent/runs/cancel.py

@@ -8,7 +8,7 @@
 from datetime import UTC, datetime
 from typing import Any, Literal, Protocol, cast
 
-from coding_agent.runtime_store import AgentRunRecord, JSONObject
+from coding_agent.stores.runtime_store import AgentRunRecord, JSONObject
 from coding_agent.stores import RuntimeRunLifecycleStore
 
 

coding-agent/src/coding_agent/runs/lifecycle.py

@@ -8,8 +8,8 @@
 from types import TracebackType
 from typing import Any, Protocol, cast
 
-from coding_agent.adapter_types import StopReason, TurnOutcome
-from coding_agent.runtime_store import AgentRunRecord, JSONObject
+from coding_agent.adapter.types import StopReason, TurnOutcome
+from coding_agent.stores.runtime_store import AgentRunRecord, JSONObject
 from coding_agent.stores import RuntimeRunLifecycleStore
 
 RuntimeRunStore = RuntimeRunLifecycleStore

coding-agent/src/coding_agent/runs/metadata.py

@@ -3,7 +3,7 @@
 from dataclasses import dataclass
 from typing import Protocol, cast
 
-from coding_agent.runtime_store import JSONObject, JSONValue
+from coding_agent.stores.runtime_store import JSONObject, JSONValue
 
 from .lifecycle import RuntimeRunResumeContext
 from .target import (

coding-agent/src/coding_agent/runs/observation.py

@@ -6,12 +6,12 @@
 from agentkit.observability import ObservationSink
 from agentkit.tape.extract import TurnTrace, extract_turns
 
-from coding_agent.agent_observability import (
+from coding_agent.observability.agent import (
     AgentObservationRecorder,
     AgentObservationStatus,
     AgentObservationStore,
 )
-from coding_agent.runtime_store import JSONObject
+from coding_agent.stores.runtime_store import JSONObject
 from coding_agent.runs.lifecycle import RuntimeRunResumeContext
 from coding_agent.runs.target import (
     RunTarget,

coding-agent/src/coding_agent/runs/persistence.py

@@ -7,7 +7,7 @@
 from math import isfinite
 from typing import Any, Protocol, cast
 
-from coding_agent.runtime_store import JSONObject, JSONValue, RunMessageSnapshotRecord
+from coding_agent.stores.runtime_store import JSONObject, JSONValue, RunMessageSnapshotRecord
 from coding_agent.stores import RuntimeCheckpointStore, RuntimeRunLifecycleStore
 
 from .lifecycle import (