fix(agent): capture Windows Bash output and pass the subprocess env

The Windows branch of `_create_bash_subprocess` spawned Git Bash with
neither pipes nor the env it was handed. `proc.stdout` and `proc.stderr`
came back `None`, so `_run_subprocess_streaming`'s reader returned
immediately and the Bash tool reported `"(no output)"` alongside the real
exit code — while the child inherited the server's own stdout/stderr and
wrote agent command output into the console and the launchd/Docker logs.

The `env` parameter was accepted and never used, so `PATH`, `VIRTUAL_ENV`,
`HOME`, `TMPDIR` and the configured import paths carried in
`ctx["subproc_env"]` never reached the child on Windows, even though every
POSIX path applies them.

Spawn it the way the POSIX path at `:688` already does: `stdin=DEVNULL`,
`stdout=PIPE`, `stderr=PIPE`, `env=env`.

`website/configuration-reference.md` is generated from source line numbers,
so the four added lines shift one entry; regenerated with
`scripts/generate_env_reference.py`.

src/agent_tools/subprocess_tools.py

@@ -117,6 +117,10 @@ async def _create_bash_subprocess(
             bash,
             "-c",
             str(command or ""),
+            stdin=asyncio.subprocess.DEVNULL,
+            stdout=asyncio.subprocess.PIPE,
+            stderr=asyncio.subprocess.PIPE,
+            env=env,
             cwd=cwd,
         )
     kwargs = {"cwd": cwd} if cwd is not None else {}