Stabilize macOS CI test timeouts

[dylan-hurd-oai]

Summary

• raise the shell snapshot apply_patch helper timeout to avoid macOS CI startup races
• increase the shared MCP app-server test read timeout so slow initialize handshakes do not fail command_exec tests spuriously

Testing

• cargo test -p codex-core shell_command_snapshot_still_intercepts_apply_patch
• cargo test -p codex-app-server command_exec_tty_implies_streaming_and_reports_pty_output