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

scripts/benchmark.py

@@ -14,8 +14,8 @@ import os
 import sys
 from pathlib import Path
 
-from nisse_core.catalog import ModelCatalog
 from nisse_core.envfile import load_env_file
+from nisse_core.models.catalog import ModelCatalog
 from nisse_dev.bench.results import append, load, render, results_file, summarise
 from nisse_dev.bench.runner import agent_commit, run_task
 from nisse_dev.bench.tasks import load_tasks

scripts/bringup.sh

@@ -133,7 +133,7 @@ cmd_logs() { journalctl -u "$UNIT" -f -o cat; }
 # The state store, read with the image's own code.
 dump() {
     docker run --rm --user 0 -v "$E2E:$E2E" --entrypoint python "$IMAGE" \
-        -m nisse_core.dump "$@"
+        -m nisse_core.state.dump "$@"
 }
 
 cmd_collect() {

scripts/ci-sshd.sh

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# The throwaway sshd the tests need (nisse_core/testing.py), in a CI job.
+# The throwaway sshd the tests need (nisse_core/execution/testing.py), in a CI job.
 # Skipped when the job's image already has it. Otherwise apt fetches from a
 # kernel.org mirror rather than archive.ubuntu.com, which has been slow
 # enough (a few KB/s) to add minutes to every job.

scripts/classifier-evals.py

@@ -19,7 +19,7 @@ import sys
 from dataclasses import asdict
 from pathlib import Path
 
-from nisse_core.canonical import StoredEvent, from_payload
+from nisse_core.log.canonical import StoredEvent, from_payload
 from nisse_dev.evals import classifier_cases
 
 

scripts/e2e.sh

@@ -36,7 +36,7 @@ else
     export NISSE_E2E_BUILD_HOST=${NISSE_E2E_BUILD_HOST:-nisse-dev.garrett-hall.com}
     export NISSE_E2E_BUILD_KEY=${NISSE_E2E_BUILD_KEY:-/root/nisse-e2e/ssh/id_ed25519}
 fi
-# Each run's state store is kept here, for nisse_core.dump after a failure.
+# Each run's state store is kept here, for nisse_core.state.dump after a failure.
 export NISSE_E2E_RUNS=${NISSE_E2E_RUNS:-/root/nisse-e2e/test-runs}
 
 # What the run spent on the test key, read from LiteLLM (spend only). The

scripts/probe_context.py

@@ -5,7 +5,7 @@
 ALIAS is a LiteLLM model alias. The LiteLLM URL and token come from the agent
 config (NISSE_CONFIG, ./nisse-dev.yaml, or --config), with its secrets from
 the environment or .env. See docs/Tuning-Guide.md, "Declaring a local model's
-limits", and nisse_core/probe.py for what the verdicts mean.
+limits", and nisse_core/models/probe.py for what the verdicts mean.
 """
 
 import argparse
@@ -15,9 +15,9 @@ from pathlib import Path
 
 import httpx
 
-from nisse_core.catalog import ModelCatalog
 from nisse_core.envfile import load_env_file
-from nisse_core.probe import probe
+from nisse_core.models.catalog import ModelCatalog
+from nisse_core.models.probe import probe
 from nisse_dev.config import AgentConfig, ConfigError