fix(cli): revert broken merge and stabilize captured process containment - #110

Reverts broken merge d58c2f2 and applies captured-process-containment runtime gates:

• Revert merge: d58c2f2
• Add: _runtime_process_output.py, _runtime_process_timing.py
• Modify: runtime commands, process cleanup, execution, outcome, start, stream, threads, run_to_file, runtime.py, test_runtime_process_containment.py

Summary by cubic

Routes run_raw and run_bytes through the same streamed containment lifecycle as the rest of the CLI, so timed-out captured subprocesses no longer leak. New _runtime_process_output.py and _runtime_process_timing.py modules own each child pipe and centralize deadline policy; captured stdout and stderr are now returned separately instead of merged, and capture and durable output are now mutually exclusive. Containment tests verify no owned descendant survives a timeout or deadline.

^{Written for commit 7d6d024. Summary will update on new commits.}