The agent loop is back to main's tool execution: it only exports runToolCall(), honors isError results, and passes structuredContent through afterToolCall. Nested calls (ctx.executeTool, ids, events with parentToolCallId, the nestedCalls record) live in coding-agent and start on the first call.
AgentSession no longer knows exec or tool_search. Tools adjust the declared loadout through a generic prepareLoadout hook, and codemode and tool_search use it like any other tool.
exec and tool_search move to built-in extensions under src/extensions/ and register inactive (defaultActive: false). The CLI loads them with MCP; SDK sessions add createCodemodeExtension(), createToolSearchExtension(), and createMcpExtension(). Extensions gain pi.getSettings() and model catalog and classifier access on ModelRegistry.