/api/shell/stream starts its PTY child under os.setsid, so the child
leads its own session and process group. The timeout, client-disconnect
and error paths all called proc.kill(), which signals only the group
leader. Creating a group and then signalling only its leader is strictly
worse than never creating one: the descendants are detached from the
server's group as well, so nothing else will ever reach them, while the
route reports "Command timed out after Ns" and exit_code -1 as if the
command were gone.
The kernel's controlling-terminal SIGHUP hid this for well-behaved
children, which is why it reads as working. Anything that ignores
SIGHUP — a nohup'ed job, a daemon, a process that means to outlive its
terminal — survives the kill indefinitely.
Signal the whole group instead, escalate to SIGKILL if it outlives the
grace period, and confirm it is actually gone. The timeout response now
says so when containment could not be established rather than claiming
a clean kill it did not get.