refactor(layout): phase2 rewrite call sites to new paths, remove shims by delete-cloud · Pull Request #596 · delete-cloud/Coding-Agent-Loop

delete-cloud · 2026-06-14T03:17:27Z

What

Phase 2 (final) of the package-layout consolidation. Now that batches 1–4 (#591/#593/#594/#595) relocated the modules behind compat shims, this PR repoints every remaining call site to the new import paths and deletes all 27 deprecation shims. Pure mechanical change — no behavior change.

102 call-site files updated (src + tests)
27 shim files removed
26 old top-level module paths repointed to their subpackage homes (coding_agent.runtime_store → coding_agent.stores.runtime_store, coding_agent.topic_* → coding_agent.topics.*, coding_agent.bee_* → coding_agent.bee.*, coding_agent.metrics → coding_agent.observability.metrics, coding_agent.app → coding_agent.core.app, etc.)
A-package names (coding_agent.observability / adapter / kb) were already real packages and are untouched.

Verification (independent, outside codex sandbox)

uv run pytest -q: 3725 passed, 8 skipped, 20 xfailed
0 shim files remain.
Repo grep for every old dotted path: no matches (the only from .metrics hit is evaluation/metrics.py, a distinct package-internal module).

Completes the consolidation: src/coding_agent/ root now holds only the package essentials + intentional cross-cutting modules (errors.py, redaction.py, tokens.py), with all subsystems in cohesive subpackages.

🤖 Generated with Claude Code

Summary by CodeRabbit

Refactor
- Internal code reorganization and module restructuring to improve package organization and remove deprecated import paths. No changes to user-facing functionality.

coderabbitai · 2026-06-14T03:17:39Z

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

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Review profile: CHILL

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Run ID: 98f2c87d-890e-4bff-a52b-c1e297e36c3d

📥 Commits

Reviewing files that changed from the base of the PR and between fff0c8c and c7fbe39.

📒 Files selected for processing (129)

coding-agent/src/coding_agent/action_safety/validation_feedback.py
coding-agent/src/coding_agent/adapter_types.py
coding-agent/src/coding_agent/agent_identity.py
coding-agent/src/coding_agent/agent_observability.py
coding-agent/src/coding_agent/app.py
coding-agent/src/coding_agent/approval/interactions.py
coding-agent/src/coding_agent/bee/launch.py
coding-agent/src/coding_agent/bee/runtime.py
coding-agent/src/coding_agent/bee/template_pack.py
coding-agent/src/coding_agent/bee/workspace.py
coding-agent/src/coding_agent/bee_command_bridge.py
coding-agent/src/coding_agent/bee_launch.py
coding-agent/src/coding_agent/bee_runtime.py
coding-agent/src/coding_agent/bee_template_pack.py
coding-agent/src/coding_agent/bee_workspace.py
coding-agent/src/coding_agent/cli/acp_command.py
coding-agent/src/coding_agent/cli/local_runtime.py
coding-agent/src/coding_agent/cli/main.py
coding-agent/src/coding_agent/cli/remote_commands.py
coding-agent/src/coding_agent/cli/stats_command.py
coding-agent/src/coding_agent/context_pack.py
coding-agent/src/coding_agent/core/app.py
coding-agent/src/coding_agent/events/display.py
coding-agent/src/coding_agent/events/replay.py
coding-agent/src/coding_agent/executors/external.py
coding-agent/src/coding_agent/external_executor.py
coding-agent/src/coding_agent/local_durable_store.py
coding-agent/src/coding_agent/local_storage.py
coding-agent/src/coding_agent/metrics.py
coding-agent/src/coding_agent/pg_durable_store.py
coding-agent/src/coding_agent/plugins/kb.py
coding-agent/src/coding_agent/plugins/memory.py
coding-agent/src/coding_agent/plugins/metrics.py
coding-agent/src/coding_agent/plugins/storage.py
coding-agent/src/coding_agent/recall_context.py
coding-agent/src/coding_agent/recall_evaluation.py
coding-agent/src/coding_agent/remote/worker.py
coding-agent/src/coding_agent/runs/attached_executor.py
coding-agent/src/coding_agent/runs/cancel.py
coding-agent/src/coding_agent/runs/lifecycle.py
coding-agent/src/coding_agent/runs/metadata.py
coding-agent/src/coding_agent/runs/observation.py
coding-agent/src/coding_agent/runs/persistence.py
coding-agent/src/coding_agent/runs/query.py
coding-agent/src/coding_agent/runs/recovery.py
coding-agent/src/coding_agent/runs/resume.py
coding-agent/src/coding_agent/runs/runtime_events.py
coding-agent/src/coding_agent/runs/scheduled.py
coding-agent/src/coding_agent/runtime_store.py
coding-agent/src/coding_agent/scheduled_runs.py
coding-agent/src/coding_agent/server/http_server.py
coding-agent/src/coding_agent/server/session_manager.py
coding-agent/src/coding_agent/storage_migration.py
coding-agent/src/coding_agent/stores/durable_local.py
coding-agent/src/coding_agent/stores/durable_pg.py
coding-agent/src/coding_agent/stores/migration.py
coding-agent/src/coding_agent/tools/subagent.py
coding-agent/src/coding_agent/topic_lifecycle.py
coding-agent/src/coding_agent/topic_memory.py
coding-agent/src/coding_agent/topic_provenance.py
coding-agent/src/coding_agent/topic_range_index.py
coding-agent/src/coding_agent/topic_recall.py
coding-agent/src/coding_agent/topic_store.py
coding-agent/src/coding_agent/topics/memory.py
coding-agent/src/coding_agent/workspace_archive.py
coding-agent/tests/cli/test_entrypoint_contract.py
coding-agent/tests/cli/test_local_runtime.py
coding-agent/tests/cli/test_remote_client.py
coding-agent/tests/coding_agent/environment/test_docker_workspace_provider.py
coding-agent/tests/coding_agent/environment/test_docker_workspace_provider_transfer.py
coding-agent/tests/coding_agent/environment/test_workspace_archive.py
coding-agent/tests/coding_agent/test_adapter_types.py
coding-agent/tests/coding_agent/test_agent_observability.py
coding-agent/tests/coding_agent/test_approval_interactions.py
coding-agent/tests/coding_agent/test_bee_command_bridge.py
coding-agent/tests/coding_agent/test_bee_launch.py
coding-agent/tests/coding_agent/test_bee_runtime.py
coding-agent/tests/coding_agent/test_bee_template_pack.py
coding-agent/tests/coding_agent/test_bee_template_pack_smoke.py
coding-agent/tests/coding_agent/test_bee_workspace.py
coding-agent/tests/coding_agent/test_bootstrap.py
coding-agent/tests/coding_agent/test_cli_pipeline.py
coding-agent/tests/coding_agent/test_context_pack.py
coding-agent/tests/coding_agent/test_cross_topic_memory_smoke.py
coding-agent/tests/coding_agent/test_display_events.py
coding-agent/tests/coding_agent/test_external_executor.py
coding-agent/tests/coding_agent/test_external_executor_smoke.py
coding-agent/tests/coding_agent/test_jsonl_runtime_store.py
coding-agent/tests/coding_agent/test_memory_review.py
coding-agent/tests/coding_agent/test_pg_durable_fencing.py
coding-agent/tests/coding_agent/test_pg_runtime_store.py
coding-agent/tests/coding_agent/test_pipeline_adapter.py
coding-agent/tests/coding_agent/test_recall_context.py
coding-agent/tests/coding_agent/test_recall_evaluation.py
coding-agent/tests/coding_agent/test_release_observability_contract.py
coding-agent/tests/coding_agent/test_run_lifecycle.py
coding-agent/tests/coding_agent/test_runtime_attached_executor_service.py
coding-agent/tests/coding_agent/test_runtime_cancel_service.py
coding-agent/tests/coding_agent/test_runtime_event_replay_service.py
coding-agent/tests/coding_agent/test_runtime_observation_service.py
coding-agent/tests/coding_agent/test_runtime_query_service.py
coding-agent/tests/coding_agent/test_runtime_resume_service.py
coding-agent/tests/coding_agent/test_runtime_run_persistence.py
coding-agent/tests/coding_agent/test_runtime_run_recovery.py
coding-agent/tests/coding_agent/test_runtime_store_contracts.py
coding-agent/tests/coding_agent/test_runtime_turn_service.py
coding-agent/tests/coding_agent/test_runtime_wire_event_recorder.py
coding-agent/tests/coding_agent/test_scheduled_runs.py
coding-agent/tests/coding_agent/test_sqlite_local_durable_fencing.py
coding-agent/tests/coding_agent/test_sqlite_runtime_store.py
coding-agent/tests/coding_agent/test_sqlite_storage_migration.py
coding-agent/tests/coding_agent/test_topic_layer_smoke.py
coding-agent/tests/coding_agent/test_topic_lifecycle.py
coding-agent/tests/coding_agent/test_topic_memory.py
coding-agent/tests/coding_agent/test_topic_provenance.py
coding-agent/tests/coding_agent/test_topic_range_index.py
coding-agent/tests/coding_agent/test_topic_recall.py
coding-agent/tests/coding_agent/test_topic_store.py
coding-agent/tests/coding_agent/tools/test_subagent.py
coding-agent/tests/conftest.py
coding-agent/tests/dogfood/test_local_dogfood_run.py
coding-agent/tests/dogfood/test_workspace_provider_demo.py
coding-agent/tests/integration/test_durable_runtime_smoke.py
coding-agent/tests/integration/test_pipeline_e2e.py
coding-agent/tests/ui/test_developer_console.py
coding-agent/tests/ui/test_http_server.py
coding-agent/tests/ui/test_session_manager_public_api.py
coding-agent/tests/ui/test_session_manager_runtime.py
coding-agent/tests/unit/core/test_metrics.py

💤 Files with no reviewable changes (27)

coding-agent/src/coding_agent/agent_identity.py
coding-agent/src/coding_agent/pg_durable_store.py
coding-agent/src/coding_agent/bee_command_bridge.py
coding-agent/src/coding_agent/bee_template_pack.py
coding-agent/src/coding_agent/topic_recall.py
coding-agent/src/coding_agent/bee_workspace.py
coding-agent/src/coding_agent/bee_launch.py
coding-agent/src/coding_agent/context_pack.py
coding-agent/src/coding_agent/topic_provenance.py
coding-agent/src/coding_agent/local_durable_store.py
coding-agent/src/coding_agent/external_executor.py
coding-agent/src/coding_agent/app.py
coding-agent/src/coding_agent/bee_runtime.py
coding-agent/src/coding_agent/adapter_types.py
coding-agent/src/coding_agent/runtime_store.py
coding-agent/src/coding_agent/topic_range_index.py
coding-agent/src/coding_agent/recall_context.py
coding-agent/src/coding_agent/storage_migration.py
coding-agent/src/coding_agent/local_storage.py
coding-agent/src/coding_agent/recall_evaluation.py
coding-agent/src/coding_agent/scheduled_runs.py
coding-agent/src/coding_agent/topic_store.py
coding-agent/src/coding_agent/metrics.py
coding-agent/src/coding_agent/workspace_archive.py
coding-agent/src/coding_agent/topic_memory.py
coding-agent/src/coding_agent/topic_lifecycle.py
coding-agent/src/coding_agent/agent_observability.py

📝 Walkthrough

Walkthrough

All deprecated sys.modules redirect shims at the flat coding_agent/ package level are removed, and every consumer across source and test files is updated to import directly from the canonical structured subpackage paths (e.g., coding_agent.stores.runtime_store, coding_agent.topics.store, coding_agent.bee.*, coding_agent.adapter.types, coding_agent.observability.agent, coding_agent.environment.archive). No functional logic changes are present.

Changes

Deprecated shim removal and call-site import updates

Layer / File(s)	Summary
Delete deprecated sys.modules redirect shims `coding-agent/src/coding_agent/adapter_types.py`, `coding-agent/src/coding_agent/agent_identity.py`, `coding-agent/src/coding_agent/agent_observability.py`, `coding-agent/src/coding_agent/app.py`, `coding-agent/src/coding_agent/bee_command_bridge.py`, `coding-agent/src/coding_agent/bee_launch.py`, `coding-agent/src/coding_agent/bee_runtime.py`, `coding-agent/src/coding_agent/bee_template_pack.py`, `coding-agent/src/coding_agent/bee_workspace.py`, `coding-agent/src/coding_agent/context_pack.py`, `coding-agent/src/coding_agent/external_executor.py`, `coding-agent/src/coding_agent/local_durable_store.py`, `coding-agent/src/coding_agent/local_storage.py`, `coding-agent/src/coding_agent/metrics.py`, `coding-agent/src/coding_agent/pg_durable_store.py`, `coding-agent/src/coding_agent/recall_context.py`, `coding-agent/src/coding_agent/recall_evaluation.py`, `coding-agent/src/coding_agent/runtime_store.py`, `coding-agent/src/coding_agent/scheduled_runs.py`, `coding-agent/src/coding_agent/storage_migration.py`, `coding-agent/src/coding_agent/topic_lifecycle.py`, `coding-agent/src/coding_agent/topic_memory.py`, `coding-agent/src/coding_agent/topic_provenance.py`, `coding-agent/src/coding_agent/topic_range_index.py`, `coding-agent/src/coding_agent/topic_recall.py`, `coding-agent/src/coding_agent/topic_store.py`, `coding-agent/src/coding_agent/workspace_archive.py`	The `sys.modules[__name__]` redirect shim bodies are removed from all flat top-level module files that previously forwarded imports to new subpackage locations.
Update source implementation import paths `coding-agent/src/coding_agent/action_safety/validation_feedback.py`, `coding-agent/src/coding_agent/approval/interactions.py`, `coding-agent/src/coding_agent/bee/launch.py`, `coding-agent/src/coding_agent/bee/runtime.py`, `coding-agent/src/coding_agent/bee/template_pack.py`, `coding-agent/src/coding_agent/bee/workspace.py`, `coding-agent/src/coding_agent/cli/`, `coding-agent/src/coding_agent/core/app.py`, `coding-agent/src/coding_agent/events/`, `coding-agent/src/coding_agent/executors/external.py`, `coding-agent/src/coding_agent/plugins/`, `coding-agent/src/coding_agent/remote/worker.py`, `coding-agent/src/coding_agent/runs/`, `coding-agent/src/coding_agent/server/`, `coding-agent/src/coding_agent/stores/`, `coding-agent/src/coding_agent/tools/subagent.py`, `coding-agent/src/coding_agent/topics/memory.py`	All source modules update their imports from deprecated flat paths to the canonical structured subpackage locations across stores, topics, bee, adapter, core, observability, and environment namespaces.
Update test import paths and monkeypatch targets `coding-agent/tests/cli/`, `coding-agent/tests/coding_agent/`, `coding-agent/tests/dogfood/`, `coding-agent/tests/integration/`, `coding-agent/tests/ui/`, `coding-agent/tests/unit/`, `coding-agent/tests/conftest.py`	All test files update their imports and monkeypatch targets to the new module paths; remote client tests also retarget archive monkeypatches from `coding_agent.workspace_archive.` to `coding_agent.environment.archive.`.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

delete-cloud/Coding-Agent-Loop#591: Touches the same legacy shim modules (workspace_archive.py, scheduled_runs.py, external_executor.py, local_durable_store.py, pg_durable_store.py, storage_migration.py) and performs the same sys.modules alias removal pattern.
delete-cloud/Coding-Agent-Loop#595: Directly precedes this PR's shim cleanup by introducing the coding_agent.topics.* subpackage layout that the shims were forwarding to.
delete-cloud/Coding-Agent-Loop#413: Added migrate_legacy_storage_to_sqlite wiring that this PR re-routes through the new coding_agent.stores.migration path while removing the coding_agent/storage_migration.py shim.

Poem

🐇 Hop, hop, the old paths are gone,
No more sys.modules tricks to rely on!
The imports now live where they truly belong,
In topics and stores, structured and strong.
The rabbit tidied each module with glee—
Clean subpackages as far as eyes see! ✨

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 10.53% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately describes the main change: completing phase 2 of package-layout consolidation by removing deprecation shims and updating call sites to new import paths.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

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Commit unit tests in branch refactor/layout-phase2-rewrite

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

c7fbe39

delete-cloud merged commit b6a0e50 into main Jun 14, 2026
2 checks passed

delete-cloud deleted the refactor/layout-phase2-rewrite branch June 14, 2026 03:41

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refactor(layout): phase2 rewrite call sites to new paths, remove shims - #596

refactor(layout): phase2 rewrite call sites to new paths, remove shims#596
delete-cloud merged 1 commit into
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refactor/layout-phase2-rewrite

delete-cloud commented Jun 14, 2026 •

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delete-cloud commented Jun 14, 2026 •

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