refactor: nuke legacy harness, drop sdk_ prefixes

The SDK harness is the only path now; legacy host-side code is gone.
File names no longer carry the ``sdk_`` distinction.

Deleted legacy host-side modules:
- strix/agents/StrixAgent/ (template moved to strix/agents/prompts/)
- strix/agents/base_agent.py, state.py
- strix/llm/llm.py, config.py
- strix/runtime/docker_runtime.py, runtime.py
- strix/tools/executor.py, agents_graph/agents_graph_actions.py
- strix/interface/sdk_dispatch.py + the env-flag dispatch in cli.py

Renamed (drop ``sdk_`` prefix):
- strix/sdk_entry.py → strix/entry.py
- strix/agents/sdk_factory.py → strix/agents/factory.py
- strix/agents/sdk_prompt.py → strix/agents/prompt.py
- strix/tools/<x>/<x>_sdk_tool[s].py → strix/tools/<x>/tool[s].py
- strix/tools/_legacy_adapter.py → strix/tools/_state_adapter.py
- ``_legacy`` aliases inside the wrappers → ``_impl``

CLI + TUI now call ``run_strix_scan`` directly — they build the
sandbox image / sources_path locally and rely on
``session_manager.cleanup`` (called inside ``run_strix_scan``'s finally)
for teardown. Three TUI handlers that reached into legacy multi-agent
globals (``_agent_instances``, ``send_user_message_to_agent``,
``stop_agent``) are now no-ops with a TODO; reconnecting them to the
``AgentMessageBus`` is a follow-up.

Tracer.get_total_llm_stats no longer reaches into the deleted
``agents_graph_actions`` globals — the orchestration hooks now feed the
tracer via ``Tracer.record_llm_usage`` (live + completed buckets).
finish_scan's ``_check_active_agents`` and load_skill's runtime
``_agent_instances`` reach-in are no-op stubs; the
``AgentMessageBus`` is the source of truth post-migration.

llm/utils.py rewritten to keep only the streaming-parser helpers
(``normalize_tool_format``, ``parse_tool_invocations``,
``fix_incomplete_tool_call``, ``format_tool_call``, ``clean_content``).
``STRIX_MODEL_MAP`` moved to ``llm/multi_provider_setup.py`` (its only
remaining caller).

Per-file ruff ignores added for legacy interface modules (TUI / main /
CLI / utils / streaming_parser / tool_components) and tracer.py —
pre-existing PLC0415/BLE001/PLR0915 patterns are out of scope.

Tests: 287/287 passing. Renamed test files to drop ``sdk_`` prefix.
``test_tracer.py::test_get_total_llm_stats_aggregates_live_and_completed``
rewritten to feed ``Tracer.record_llm_usage`` instead of legacy globals.
Test file annotations added so pre-commit's strict mypy passes.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

strix/tools/notes/tools.py

@@ -0,0 +1,117 @@
+"""SDK function-tool wrappers for the legacy notes tools.
+
+Five tools, all module-global (no per-agent silo). The legacy
+``notes_actions.py`` module already implements JSONL persistence and
+wiki Markdown rendering; these wrappers are pure delegation.
+
+The C6 fix (lock-protected JSONL writes) was applied directly to the
+legacy module, so both code paths benefit.
+"""
+
+from __future__ import annotations
+
+import asyncio
+import json
+from typing import Any
+
+from agents import RunContextWrapper
+
+from strix.tools._decorator import strix_tool
+from strix.tools.notes import notes_actions as _impl
+
+
+def _dump(result: dict[str, Any]) -> str:
+    return json.dumps(result, ensure_ascii=False, default=str)
+
+
+@strix_tool(timeout=30)
+async def create_note(
+    ctx: RunContextWrapper,
+    title: str,
+    content: str,
+    category: str = "general",
+    tags: list[str] | None = None,
+) -> str:
+    """Create a note in the current run's notes store.
+
+    Notes are persisted to ``run_dir/notes/notes.jsonl`` and (for the
+    ``wiki`` category) rendered as Markdown to ``run_dir/wiki/<slug>.md``.
+
+    Args:
+        title: Required, non-empty title.
+        content: Note body. Markdown is preserved.
+        category: One of ``"general" | "findings" | "methodology" |
+            "questions" | "plan" | "wiki"``.
+        tags: Optional list of free-form tags.
+    """
+    # The legacy function does file I/O under a threading.RLock.
+    # Wrap in to_thread so we don't block the event loop while waiting
+    # on the lock or fsync.
+    result = await asyncio.to_thread(
+        _impl.create_note,
+        title=title,
+        content=content,
+        category=category,
+        tags=tags,
+    )
+    return _dump(result)
+
+
+@strix_tool(timeout=30)
+async def list_notes(
+    ctx: RunContextWrapper,
+    category: str | None = None,
+    tags: list[str] | None = None,
+    search: str | None = None,
+    include_content: bool = False,
+) -> str:
+    """List notes, optionally filtered.
+
+    Args:
+        category: Filter by category.
+        tags: Filter to notes that have any of these tags.
+        search: Substring match against title and content.
+        include_content: When False (default), entries get a ``content_preview``;
+            when True, full content is included.
+    """
+    result = await asyncio.to_thread(
+        _impl.list_notes,
+        category=category,
+        tags=tags,
+        search=search,
+        include_content=include_content,
+    )
+    return _dump(result)
+
+
+@strix_tool(timeout=30)
+async def get_note(ctx: RunContextWrapper, note_id: str) -> str:
+    """Fetch one note by its 5-char ID. Returns full content."""
+    result = await asyncio.to_thread(_impl.get_note, note_id=note_id)
+    return _dump(result)
+
+
+@strix_tool(timeout=30)
+async def update_note(
+    ctx: RunContextWrapper,
+    note_id: str,
+    title: str | None = None,
+    content: str | None = None,
+    tags: list[str] | None = None,
+) -> str:
+    """Update a note's title, content, or tags. Pass ``None`` to leave a field unchanged."""
+    result = await asyncio.to_thread(
+        _impl.update_note,
+        note_id=note_id,
+        title=title,
+        content=content,
+        tags=tags,
+    )
+    return _dump(result)
+
+
+@strix_tool(timeout=30)
+async def delete_note(ctx: RunContextWrapper, note_id: str) -> str:
+    """Delete a note. For wiki notes, also removes the rendered Markdown file."""
+    result = await asyncio.to_thread(_impl.delete_note, note_id=note_id)
+    return _dump(result)