[Feature] Adding a CLI timeout flag and unit tests

[antonio-amjr]

Fix: project-chip/certification-tool#1038
Related to: project-chip/certification-tool-backend#356

Description

Lets users override the prompt timeout for a single run without editing the project's JSON config.

Changed

• commands/run_tests.py: new --prompt-timeout SECONDS option; merges {"th_config": {"prompt_timeout_seconds": N}} into the execution config via the existing merge_configs(). Execution-only, not persisted; wins over any value from --config.

Test plan

• New tests in test_run_tests.py: flag merges into execution config standalone, and takes precedence when combined with --config.
• New test_utils.py case illustrating a th_config merge.
• Please run pytest tests/test_run_tests.py tests/test_utils.py before merging.

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