feat(R05): tool capability registry, unified policy gateway, MCP lifecycle manager

EPIC R05 (Team Hoa) - one security/approval path for every tool call.

R05-T01 domain/tools/{tool_descriptor,tool_registry}.py
  ToolCapability (READ/WRITE/EXECUTE/NETWORK, composable) + ToolDescriptor +
  ToolRegistry, replacing three independently-maintained gating lists
  (core/tools.py::WRITE_TOOLS, code_agent.py's WRITE_TOOLS|MS365_WRITE_TOOLS,
  chat_agent.py's literal ("run_command","install_package") tuple) with one
  capability lookup.

R05-T02 infrastructure/filesystem/{file_tools,command_tools,fetch_tools,tool_context}.py
  core/tools.py's execute_tool if/elif chain split into per-concern modules.
  core/tools.py is now a strangler-fig shim: re-exports ToolContext/ToolError,
  dispatches through a {name: handler} dict built from the split modules.
  core/tools.py: 566 -> 291 lines.

R05-T03 application/conversations/tool_policy_gateway.py
  ToolPolicyGateway.allow(name, gate, payload) - capability-driven ALLOW vs
  ask-the-gate decision. Wired into both chat_agent.py::run_cowork and
  code_agent.py::run_code, replacing their separate hand-rolled checks.
  Verified equivalent to the old hardcoded sets by test.

R05-T04 (behavior change, not just refactor)
  MCP/connector tools (core/mcp_client.py, core/ext_connectors.py) reached
  chat_agent.py via extra_executor(name, args) with NO permission check at
  all. They are now tagged with a conservative default capability
  (WRITE|EXECUTE|NETWORK - no MCP tool self-declares risk) and routed through
  the SAME ToolPolicyGateway as built-ins. When "confirm before running
  commands" is on, MCP/connector calls now prompt like run_command already
  did - a real gap closed, and a user-visible change worth calling out.

R05-T05 infrastructure/mcp/mcp_source_manager.py
  McpToolSourceManager extracts the connection cache/lock/start-or-skip
  lifecycle out of state.py::AppContext (_mcp_connections/_conn_lock) into a
  standalone, directly-testable class. AppContext.build_mcp_tools and
  _ms365_builtin_connection now call ensure()/stop(); _ext_connections
  (unified Connectors) is out of scope for this task and keeps its own lock.

New tests: tests/unit/test_tool_registry_and_policy.py,
test_code_agent_tool_policy.py, test_cowork_extra_tool_policy.py,
test_mcp_source_manager.py (26 new tests).

Suite: 254 passed, 4 pre-existing failures unrelated to R05 (2 EPIC R02
config-security, 2 environment-dependent routing tests - see checklist).
check_imports: PASS. All new files < 400 LOC.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

infrastructure/filesystem/tool_context.py

@@ -0,0 +1,62 @@
+"""ToolContext / ToolError / CancelFn - the sandboxed execution context every
+built-in tool runs against (moved out of ``core/tools.py`` in R05-T02).
+
+Kept as its own leaf module (no dependency on any sibling in this package) so
+``file_tools.py``, ``command_tools.py`` and ``fetch_tools.py`` can each import
+it without creating an import cycle back through ``core/tools.py``, which
+itself re-exports ``ToolContext``/``ToolError`` from here for the existing
+callers (``core/chat_agent.py``, ``core/code_agent.py``,
+``core/task_executors.py``) that do ``from .tools import ToolContext``.
+"""
+from __future__ import annotations
+
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Any, Callable, Dict, Optional
+
+CancelFn = Callable[[], bool]
+
+
+class ToolError(Exception):
+    pass
+
+
+@dataclass
+class ToolContext:
+    workdir: Path
+    flatten_writes: bool = False  # Cowork: force every write into the workdir root
+    sandbox: bool = False  # Code tab: isolate run_command/install_package into <workdir>/.venv
+    # Sandbox Security Layer — Settings' "Resource Limits" (cpu_percent/memory_mb/
+    # disk_mb), applied to every run_command/install_package this context runs.
+    # None (default) = no limits, matching pre-existing behavior.
+    resource_limits: Optional[Dict[str, float]] = None
+    # Sandbox Security Layer — Settings' "Block network for agent commands"
+    # (policy-level, see deps.py::network_blocked_env). False (default) =
+    # unrestricted, matching pre-existing behavior.
+    block_network: bool = False
+    # Whether the fetch_url tool may read URLs — SEPARATE from block_network
+    # (reading a web page/share link for info is safe; running networked shell
+    # commands is the risk). Defaults True; set from agent_security.allow_url_fetch.
+    allow_url_fetch: bool = True
+    # Jira read connector config (base_url/email/api_token) — None disables the
+    # jira_* tools' ability to connect. Populated from config.data["jira"].
+    jira: Optional[Dict[str, Any]] = None
+
+    def resolve(self, rel: str) -> Path:
+        """Resolve ``rel`` inside the workdir, rejecting escapes."""
+        if rel in ("", "."):
+            return self.workdir
+        candidate = (self.workdir / rel).expanduser()
+        try:
+            resolved = candidate.resolve()
+        except OSError as exc:
+            raise ToolError(f"Invalid path: {rel} ({exc})")
+        root = self.workdir.resolve()
+        if resolved != root and root not in resolved.parents:
+            raise ToolError(
+                f"Refused: '{rel}' is outside the working folder ({root})."
+            )
+        return resolved
+
+
+__all__ = ["CancelFn", "ToolError", "ToolContext"]