fix: Enforce timeout_ms in shell and shell_command to prevent orphan processes #145

Summary

shell / shell_command expose timeout_ms, but the value is currently passed as yield_time_ms and does not terminate execution. This can return a running session and leave a process alive without a continuation path in shell-only mode.

• Affected code: /Users/mcell/Desktop/workspace/memo-cli/packages/tools/src/tools/shell.ts:34
• Affected code: /Users/mcell/Desktop/workspace/memo-cli/packages/tools/src/tools/shell_command.ts:26
• Runtime behavior source: /Users/mcell/Desktop/workspace/memo-cli/packages/tools/src/tools/exec_runtime.ts:238

Why this matters

• API contract confusion: timeout_ms implies command timeout, not just response wait window.
• Resource leak risk: processes continue running after tool call returns.
• In MEMO_SHELL_TOOL_TYPE=shell|shell_command, there is no write_stdin tool to manage returned session IDs.

Repro

Call:

• shell_command.execute({ command: 'sleep 2; echo done', login: false, timeout_ms: 100 })

Observed:

• Returns in ~100ms with Process running with session ID ...
• Does not fail on timeout
• Process continues beyond timeout window

Expected

timeout_ms should enforce an execution deadline (kill process and return timeout error or explicit timeout status).

Actual

It only controls wait duration before returning intermediate output.

Suggested fix

• Add real timeout handling in runtime (timer + signal/kill + deterministic timeout response).
• Keep yield_time_ms as separate parameter for streaming semantics.
• Add tests for timeout termination and shell-only mode behavior.

Requested implementer

Please let memo handle this fix.