Fix pre-parse JSON flag detection (#212)

[codeforester]

Summary

• Parse combined positive/negative JSON lifecycle declarations consistently with the rest of the lifecycle flags.
• Let the last explicit JSON flag override the configured default before pre-parse errors are rendered.
• Add regression coverage for combined declarations and explicit --no-json with a true default.

Validation

• uv run --extra dev --extra typer --extra quality pytest tests/test_json_contracts.py -q
• uv run --extra quality ruff format --check lib/python/base_cli/app.py tests/test_json_contracts.py
• uv run --extra quality ruff check lib/python/base_cli/app.py tests/test_json_contracts.py
• uv run --extra quality mypy lib/python/base_cli/app.py

Closes #212.