nisse-core: group modules into packages by architecture section

A pure move; behaviour unchanged.

- models (L9, L7): llm, catalog, probe, render, render_anthropic, context
- log (L7, L6): canonical, views
- state (L8): store (was state), reconcile, worker, cancel, dump
- knowledge (L10, L6.4): vault, memory
- conversation (L5): transport, matrix
- execution (L13): ssh (was execution), testing
- authority (P3, P4, L4): actions
- gitea, oplog, envfile stay at the top until each gains a second module.

Every import, monkeypatch target, script and doc reference rewritten.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01J5Utyfzw7gF7UhjRDEtjTk

tests/integration/conftest.py

@@ -15,7 +15,7 @@ import pytest
 
 from nisse_core.envfile import load_env_file
 from nisse_core.gitea import GiteaClient
-from nisse_core.llm import AnthropicPassthroughClient, LiteLLMClient
+from nisse_core.models.llm import AnthropicPassthroughClient, LiteLLMClient
 from nisse_dev.config import AgentConfig
 
 REPO = Path(__file__).resolve().parents[2]

tests/integration/e2e_support.py

@@ -10,9 +10,9 @@ from collections.abc import Iterator
 from dataclasses import dataclass
 from pathlib import Path
 
-from nisse_core.execution import SSHHost
+from nisse_core.execution.ssh import SSHHost
 from nisse_core.gitea import GiteaClient, GiteaError
-from nisse_core.llm import RoleMap
+from nisse_core.models.llm import RoleMap
 from nisse_dev.config import BuildHost
 
 # The end-to-end tests run every role on a local model, which costs nothing

tests/integration/test_benchmark_live.py

@@ -5,8 +5,8 @@ from pathlib import Path
 
 import pytest
 
-from nisse_core.catalog import ModelCatalog
-from nisse_core.execution import SSHHost
+from nisse_core.execution.ssh import SSHHost
+from nisse_core.models.catalog import ModelCatalog
 from nisse_dev.bench.runner import run_task
 from nisse_dev.bench.tasks import load_tasks
 from nisse_dev.config import AgentConfig

tests/integration/test_classifier_cases.py

@@ -15,8 +15,8 @@ from typing import Any
 import pytest
 import yaml
 
-from nisse_core.actions import Action
-from nisse_core.llm import LiteLLMClient
+from nisse_core.authority.actions import Action
+from nisse_core.models.llm import LiteLLMClient
 from nisse_dev.loop.classifier import ActionClassifier, Scope
 
 pytestmark = pytest.mark.integration

tests/integration/test_crash_durability.py

@@ -7,7 +7,7 @@ from pathlib import Path
 
 import pytest
 
-from nisse_core.reconcile import reconcile_on_boot
+from nisse_core.state.reconcile import reconcile_on_boot
 from nisse_dev.state import StateStore
 
 pytestmark = pytest.mark.integration
@@ -15,7 +15,7 @@ pytestmark = pytest.mark.integration
 CRASH_SCRIPT = """
 import os
 import sys
-from nisse_core.canonical import UserMessage
+from nisse_core.log.canonical import UserMessage
 from nisse_dev.state import StateStore
 
 store = StateStore(sys.argv[1])

tests/integration/test_delegation_live.py

@@ -6,8 +6,8 @@ from pathlib import Path
 
 import pytest
 
-from nisse_core.execution import SSHHost
-from nisse_core.llm import AnthropicPassthroughClient
+from nisse_core.execution.ssh import SSHHost
+from nisse_core.models.llm import AnthropicPassthroughClient
 from nisse_core.oplog import OpLog
 from nisse_dev.delegation import Caps, Delegation
 from nisse_dev.git import GitRepo

tests/integration/test_end_to_end_loop.py

@@ -31,10 +31,10 @@ from e2e_support import (
     task,
 )
 
-from nisse_core.canonical import ActionVerdict
-from nisse_core.execution import SSHHost
+from nisse_core.conversation.transport import InMemoryTransport
+from nisse_core.execution.ssh import SSHHost
 from nisse_core.gitea import GiteaClient, GiteaError
-from nisse_core.transport import InMemoryTransport
+from nisse_core.log.canonical import ActionVerdict
 from nisse_dev.config import AgentConfig, LoopTuning
 from nisse_dev.loop import preflight
 from nisse_dev.loop.build import RunningLoop, build_loop_agent
@@ -71,7 +71,7 @@ def running(
     run = uuid.uuid4().hex[:8]
     stack = contextlib.ExitStack()
     # Kept outside pytest's temp directories, which pytest prunes, so a
-    # failed run's transcript can be read afterwards (nisse_core.dump).
+    # failed run's transcript can be read afterwards (nisse_core.state.dump).
     keep = Path(os.environ.get("NISSE_E2E_RUNS", "/tmp/nisse-e2e-runs")) / run
     keep.mkdir(parents=True, exist_ok=True)
     print(f"\ne2e run {run}: state store in {keep}")

tests/integration/test_expert_live.py

@@ -9,7 +9,7 @@ from pathlib import Path
 
 import pytest
 
-from nisse_core.llm import LiteLLMClient, RoleMap
+from nisse_core.models.llm import LiteLLMClient, RoleMap
 from nisse_core.oplog import OpLog
 from nisse_dev.evals import collect
 from nisse_dev.expert import BudgetExhausted, ExpertDesk

tests/integration/test_gitea_live.py

@@ -9,9 +9,9 @@ from pathlib import Path
 import pytest
 from e2e_support import fresh_repo, operator_gitea
 
-from nisse_core.execution import SSHHost
+from nisse_core.execution.ssh import SSHHost
 from nisse_core.gitea import GiteaClient, pull_request_reconciler
-from nisse_core.state import Intent
+from nisse_core.state.store import Intent
 from nisse_dev.config import AgentConfig
 from nisse_dev.git import GitError, GitRepo, SSHKey
 from nisse_dev.loop.build import remote_url

tests/integration/test_llm_live.py

@@ -2,10 +2,10 @@
 
 import pytest
 
-from nisse_core.canonical import AssistantText, StoredEvent, UserMessage
-from nisse_core.catalog import ModelCatalog
-from nisse_core.context import BudgetedClient
-from nisse_core.llm import LiteLLMClient
+from nisse_core.log.canonical import AssistantText, StoredEvent, UserMessage
+from nisse_core.models.catalog import ModelCatalog
+from nisse_core.models.context import BudgetedClient
+from nisse_core.models.llm import LiteLLMClient
 from nisse_dev.config import AgentConfig
 
 pytestmark = pytest.mark.integration

tests/integration/test_matrix_live.py

@@ -5,7 +5,7 @@ import uuid
 
 import pytest
 
-from nisse_core.matrix import MatrixConfig, MatrixTransport
+from nisse_core.conversation.matrix import MatrixConfig, MatrixTransport
 from nisse_dev.config import AgentConfig
 
 pytestmark = pytest.mark.integration

tests/integration/test_model_capability.py

@@ -21,15 +21,15 @@ argument, not configuration.
 
 import pytest
 
-from nisse_core.canonical import (
+from nisse_core.log.canonical import (
     AssistantText,
     StoredEvent,
     ToolCall,
     ToolResult,
     UserMessage,
 )
-from nisse_core.catalog import ModelCatalog, select_client
-from nisse_core.llm import AnthropicPassthroughClient, LiteLLMClient, LLMError
+from nisse_core.models.catalog import ModelCatalog, select_client
+from nisse_core.models.llm import AnthropicPassthroughClient, LiteLLMClient, LLMError
 from nisse_dev.config import AgentConfig
 from nisse_dev.expert import parse_answer
 from nisse_dev.loop.tools import ASK_HUMAN, FINISH_MILESTONE, RESTATE

tests/integration/test_passthrough_live.py

@@ -11,8 +11,8 @@ from pathlib import Path
 import httpx
 import pytest
 
-from nisse_core.canonical import AssistantText, ToolCall, ToolResult, UserMessage
-from nisse_core.llm import AnthropicPassthroughClient
+from nisse_core.log.canonical import AssistantText, ToolCall, ToolResult, UserMessage
+from nisse_core.models.llm import AnthropicPassthroughClient
 from nisse_core.oplog import OpLog
 from nisse_dev.config import AgentConfig
 from nisse_dev.state import StateStore