docs: Address 8 architectural review findings in code executor design doc

Add Non-Goals & Invariants section, fix append-before-execute state
poisoning, redesign timeout as per-invocation field on CodeExecutionInput,
use Docker exec kill instead of thread+join for container timeout,
replace preexec_fn with process_group, pin default container image digest,
reframe restricted builtins as best-effort friction, document execution_id
gap in ExecuteSkillScriptTool.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: caohy1988