fix(tools): address PR review — remove _extract_raw_output, BudgetConfig everywhere, read_file hardening

- Remove _extract_raw_output: persist content verbatim (fixes size mismatch bug)
- Drop import aliases: import from budget_config directly, one canonical name
- BudgetConfig param on maybe_persist_tool_result and enforce_turn_budget
- read_file: limit=None signature, pre-read guard fires only when limit omitted (256KB)
- Unify binary extensions: file_operations.py imports from binary_extensions.py
- Exclude .pdf and .svg from binary set (text-based, agents may inspect)
- Remove redundant outer try/except in eval path (internal fallback handles it)
- Fix broken tests: update assertion strings for new persistence format
- Module-level constants: _PRE_READ_MAX_BYTES, _DEFAULT_READ_LIMIT
- Remove redundant pathlib import (Path already at module level)
- Update spec.md with IMPLEMENTED annotations and design decisions

tests/run_agent/test_run_agent.py

@@ -1011,10 +1011,9 @@ class TestExecuteToolCalls:
         big_result = "x" * 150_000
         with patch("run_agent.handle_function_call", return_value=big_result):
             agent._execute_tool_calls(mock_msg, messages, "task-1")
-        # Content should be replaced with preview + file path
+        # Content should be replaced with persisted-output or truncation
         assert len(messages[0]["content"]) < 150_000
-        assert "Large tool response" in messages[0]["content"]
-        assert "Full output saved to:" in messages[0]["content"]
+        assert ("Truncated" in messages[0]["content"] or "<persisted-output>" in messages[0]["content"])
 
 
 class TestConcurrentToolExecution:
@@ -1249,8 +1248,7 @@ class TestConcurrentToolExecution:
         assert len(messages) == 2
         for m in messages:
             assert len(m["content"]) < 150_000
-            assert "Large tool response" in m["content"]
-            assert "Full output saved to:" in m["content"]
+            assert ("Truncated" in m["content"] or "<persisted-output>" in m["content"])
 
     def test_invoke_tool_dispatches_to_handle_function_call(self, agent):
         """_invoke_tool should route regular tools through handle_function_call."""