Add JSON output for basectl doctor

[codeforester]

Summary

• Add --format text|json support to basectl doctor.
• Emit structured Base doctor findings with status, name, message, and fix fields.
• Teach the base_dev and base_setup Python doctor paths to emit JSON findings too.
• Compose project and developer prerequisite doctor findings into dev_findings and project_findings sections.
• Add Bash integration tests and Python unit coverage, and remove the completed TODO item.

Validation

• bats cli/bash/commands/basectl/tests/basectl.bats
• bats cli/bash/commands/basectl/tests/setup.bats
• bash -n cli/bash/commands/basectl/subcommands/doctor.sh
• bash -n cli/bash/commands/basectl/subcommands/setup_common.sh
• env PYTHONPATH=lib/python:cli/python ~/.base.d/base/.venv/bin/python -m pytest cli/python/base_setup/tests/test_engine.py
• env PYTHONPATH=lib/python:cli/python ~/.base.d/base/.venv/bin/python -m pytest cli/python/base_dev/tests/test_engine.py
• env PYTHONPATH=lib/python:cli/python ~/.base.d/base/.venv/bin/python -m pylint --rcfile=.pylintrc cli/python/base_dev/engine.py cli/python/base_setup/engine.py cli/python/base_dev/tests/test_engine.py cli/python/base_setup/tests/test_engine.py
• bin/basectl doctor --format json
• git diff --check