fix: add timeout to subprocess.run() and proc.wait() calls

subprocess.run() and proc.wait() without timeout can hang indefinitely
if the child process becomes unresponsive. This blocks the calling
thread forever.

Fixed locations:
- tools/transcription_tools.py: ffmpeg conversion (timeout=300) and
  user-configured STT commands with shell=True (timeout=300)
- gateway/run.py: helper script proc.wait() (timeout=3600)

Not fixed:
- agent/anthropic_adapter.py: interactive 'claude setup-token' —
  user-driven, timeout would be inappropriate

gateway/run.py

@@ -15126,7 +15126,7 @@ class GatewayRunner:
                     env["PYTHONUNBUFFERED"] = "1"
                     with open(output_path, "wb") as f:
                         proc = subprocess.Popen(cmd, stdout=f, stderr=subprocess.STDOUT, env=env)
-                        rc = proc.wait()
+                        rc = proc.wait(timeout=3600)
                     with open(exit_code_path, "w") as f:
                         f.write(str(rc))
                     """