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

[marlon-costa-dc]

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

Reverts the broken CLI merge that destabilized the runtime, then adds containment gates so captured subprocesses no longer leak during cleanup or streaming. The revert restores the pre-merge agent tooling and lint configuration. New _runtime_process_output.py and _runtime_process_timing.py modules centralize process handling, and containment tests now cover the new gates.

^{Written for commit f9c11fc. Summary will update on new commits.}

[sonarqubecloud]

Quality Gate failed

Failed conditions
E Security Rating on New Code (required ≥ A)

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