refactor(tools): migrate execution logic to src/agent_tools/ package with handler registry (#3435)

* refactor(tools): implement strict cohesive class coordinator pattern per #2917

* test: update edit_file tests to use EditFileTool class

* fix(tools): restore tool_policy param and security backstop in coordinator

* refactor(tools): migrate domain tools to agent_tools package per #2917

* test: update test imports for new agent_tools package

* fix: resolve circular import between tool_execution and agent_tools

* fix: remove leftover git conflict markers

* fix(tools): resolve pytest failure and document _apply method

* fix(tools): clean up whitespace and remove dead _tool_python helper

---------

Co-authored-by: Alexandre Teixeira <111787685+alteixeira20@users.noreply.github.com>

src/agent_tools/subprocess_tools.py

@@ -0,0 +1,155 @@
+import asyncio
+import sys
+import time
+import collections
+from typing import Optional, Callable, Awaitable, Tuple, Dict
+from src.constants import MAX_OUTPUT_CHARS
+
+DEFAULT_BASH_TIMEOUT = 60 * 60     # 1 hour
+DEFAULT_PYTHON_TIMEOUT = 60 * 60
+
+PROGRESS_INTERVAL_S = 2.0
+PROGRESS_TAIL_LINES = 12
+
+async def _run_subprocess_streaming(
+    proc: asyncio.subprocess.Process,
+    *,
+    timeout: float,
+    progress_cb: Optional[Callable[[Dict], Awaitable[None]]] = None,
+) -> Tuple[str, str, Optional[int], bool]:
+    started = time.time()
+    stdout_full: list[str] = []
+    stderr_full: list[str] = []
+    tail = collections.deque(maxlen=PROGRESS_TAIL_LINES)
+
+    async def _reader(stream, full_buf, label: str):
+        if stream is None:
+            return
+        while True:
+            line = await stream.readline()
+            if not line:
+                break
+            decoded = line.decode("utf-8", errors="replace").rstrip("\n")
+            full_buf.append(decoded)
+            if label == "err":
+                tail.append(f"! {decoded}")
+            else:
+                tail.append(decoded)
+
+    async def _progress_emitter():
+        await asyncio.sleep(PROGRESS_INTERVAL_S)
+        while True:
+            if progress_cb:
+                try:
+                    await progress_cb({
+                        "elapsed_s": round(time.time() - started, 1),
+                        "tail": "\n".join(list(tail)),
+                    })
+                except Exception:
+                    pass
+            await asyncio.sleep(PROGRESS_INTERVAL_S)
+
+    rd_out = asyncio.create_task(_reader(proc.stdout, stdout_full, "out"))
+    rd_err = asyncio.create_task(_reader(proc.stderr, stderr_full, "err"))
+    prog_task = asyncio.create_task(_progress_emitter()) if progress_cb else None
+
+    timed_out = False
+    try:
+        await asyncio.wait_for(proc.wait(), timeout=timeout)
+    except asyncio.TimeoutError:
+        timed_out = True
+        try:
+            proc.kill()
+        except Exception:
+            pass
+        try:
+            await asyncio.wait_for(proc.wait(), timeout=2)
+        except Exception:
+            pass
+    except asyncio.CancelledError:
+        try:
+            proc.kill()
+        except Exception:
+            pass
+        try:
+            await asyncio.wait_for(proc.wait(), timeout=2)
+        except Exception:
+            pass
+        for t in (rd_out, rd_err):
+            t.cancel()
+        if prog_task is not None:
+            prog_task.cancel()
+        raise
+    finally:
+        if prog_task is not None and not prog_task.done():
+            prog_task.cancel()
+            try:
+                await prog_task
+            except (asyncio.CancelledError, Exception):
+                pass
+        for t in (rd_out, rd_err):
+            try:
+                await asyncio.wait_for(t, timeout=1)
+            except Exception:
+                pass
+
+    return (
+        "\n".join(stdout_full),
+        "\n".join(stderr_full),
+        proc.returncode,
+        timed_out,
+    )
+
+class BashTool:
+    async def execute(self, content: str, ctx: dict) -> dict:
+        from src.tool_execution import _AGENT_WORKDIR, _truncate
+        progress_cb = ctx.get("progress_cb")
+        workspace = ctx.get("workspace")
+        _subproc_env = ctx.get("subproc_env")
+        proc = await asyncio.create_subprocess_shell(
+            content,
+            stdout=asyncio.subprocess.PIPE,
+            stderr=asyncio.subprocess.PIPE,
+            env=_subproc_env,
+            cwd=workspace or _AGENT_WORKDIR,
+        )
+        stdout, stderr, rc, timed_out = await _run_subprocess_streaming(
+            proc,
+            timeout=DEFAULT_BASH_TIMEOUT,
+            progress_cb=progress_cb,
+        )
+        if timed_out:
+            return {"error": f"bash: timed out after {DEFAULT_BASH_TIMEOUT}s — process killed", "exit_code": 124, "stdout": _truncate(stdout, MAX_OUTPUT_CHARS), "stderr": _truncate(stderr, MAX_OUTPUT_CHARS)}
+        output = stdout.rstrip()
+        err = stderr.rstrip()
+        if err:
+            output = (output + "\nSTDERR: " + err).strip() if output else "STDERR: " + err
+        output = _truncate(output, MAX_OUTPUT_CHARS)
+        return {"output": output or "(no output)", "exit_code": rc or 0}
+
+class PythonTool:
+    async def execute(self, content: str, ctx: dict) -> dict:
+        from src.tool_execution import _AGENT_WORKDIR, _truncate
+        progress_cb = ctx.get("progress_cb")
+        workspace = ctx.get("workspace")
+        _subproc_env = ctx.get("subproc_env")
+        proc = await asyncio.create_subprocess_exec(
+            (sys.executable or "python"), "-I", "-c", content,
+            stdout=asyncio.subprocess.PIPE,
+            stderr=asyncio.subprocess.PIPE,
+            env=_subproc_env,
+            cwd=workspace or _AGENT_WORKDIR,
+        )
+        stdout, stderr, rc, timed_out = await _run_subprocess_streaming(
+            proc,
+            timeout=DEFAULT_PYTHON_TIMEOUT,
+            progress_cb=progress_cb,
+        )
+        if timed_out:
+            return {"error": f"python: timed out after {DEFAULT_PYTHON_TIMEOUT}s — process killed", "exit_code": 124, "stdout": _truncate(stdout, MAX_OUTPUT_CHARS), "stderr": _truncate(stderr, MAX_OUTPUT_CHARS)}
+        output = stdout.rstrip()
+        err = stderr.rstrip()
+        if err:
+            output = (output + "\nSTDERR: " + err).strip() if output else "STDERR: " + err
+        output = _truncate(output, MAX_OUTPUT_CHARS)
+        return {"output": output or "(no output)", "exit_code": rc or 0}