Add spec-aware subnet checks to netengine doctor

[aidankhogg]

Motivation

• Enable users to validate requested world subnets before bootstrapping so Docker networks that would reuse or overlap world subnets are detected early.
• Allow netengine doctor to be run against a world spec to include spec.substrate.networks[*].subnet in preflight network checks.
• Provide clearer diagnostics and remediation when an existing Docker network reuses or overlaps a requested subnet.

Description

• Added an optional --spec PATH option and an optional positional spec argument to the doctor command in netengine/cli/doctor.py, with mutual-exclusion handling and spec-loading via the existing spec loader.
• Extended DoctorContext and the preflight API (build_context, run_checks) in netengine/diagnostic/preflight.py to carry spec_subnets: tuple[str, ...] through preflight probes.
• Updated _check_docker_subnet_conflicts to collect compose-defined subnets and also include ctx.spec_subnets, to detect overlaps and exact reuse and to emit clearer conflict messages and remediation hints referencing Docker network names.
• Plumbed spec subnet extraction into the readiness flow in netengine/cli/main.py so readiness uses the loaded spec's substrate subnets for subnet checks.
• Documented usage in README.md, docs/alpha-quickstart.md, and docs/troubleshooting.md with examples like poetry run netengine doctor --spec examples/minimal.yaml.
• Added unit tests in tests/test_doctor.py covering --spec handling and Docker subnet conflict detection against spec subnets, and formatted/linted modified files.

Testing

• Ran python -m pytest tests/test_doctor.py and all tests passed (15 passed).
• Ran python -m ruff check on modified files and linting completed with no issues (All checks passed).
• Ran git diff --check to verify no whitespace/git-diff problems and none were reported.

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Codex Task