Promote ROBOT/ELK validation to default ontology build path

[mzargham]

Context

The current make ontology target runs a Python-only build. ROBOT-based validation (ELK reasoning + OBO hygiene) is gated behind the optional make ontology-robot target, which requires Java + obo-robot. The Stage 0 banner prints Validation: Python build (run make ontology-robot for ELK + report).

For the JAXA workshop talk (June 12 2026), we want ROBOT to be part of the canonical build path — not an opt-in — so the integration story holds: the assembled ontology is audited at build time by ROBOT/ELK against the upstream vendored imports.

Current state

• make ontology → Python-only build (default)
• make ontology-robot → optional ROBOT merge + ELK reason + report
• Stage 0 banner reflects Python build by default
• No CI step runs ROBOT

Proposed change

• Make ROBOT the default validator inside make ontology when Java + obo-robot are available on the path
• Decide and document failure mode when the toolchain is missing (fail-fast vs. loud-warn-and-fallback)
• Update Stage 0 banner to print the ROBOT result on default builds
• Wire ROBOT into CI on every push and PR

Acceptance criteria

• make ontology runs ROBOT/ELK reasoning + OBO report when toolchain present
• Behavior on missing toolchain is explicit, documented, and tested
• Stage 0 banner shows ROBOT outcome on default builds
• CI runs ROBOT on every push to main and on PRs
• README updated: ROBOT is the default; Python-only is the no-Java fallback
• Tests cover both paths (ROBOT available, ROBOT missing)

[mzargham]

Resolved by WP2 merge (commit eec771c, merged to staging in d3c417c)

All five acceptance criteria covered:

• make ontology runs ROBOT/ELK reasoning + OBO report when toolchain present
• Behavior on missing toolchain is fail-fast (per the "stop being a mock-up" roadmap directive); error message points users at make ontology-python as the explicit no-Java path; documented in README + CLAUDE.md
• Stage 0 banner shows ROBOT outcome on default builds (Verification: ROBOT merge + ELK reasoning + OBO report PASS)
• CI runs ROBOT on every push to main/staging and on PRs (.github/workflows/ontology.yml; setup-java@v4 + cached robot.jar)
• README updated: ROBOT is the default; make ontology-python is the documented fallback for no-Java environments
• Tests cover both paths (ROBOT available, ROBOT missing)

WP2 also bundled: pytest live/network markers, triple-count budget gate (380 → 450 after WP4), and the openCAESAR code/data cleanup (CSV column + constant rename + rtm.ttl regeneration). All on staging.

JAXA workshop deadline (2026-06-12) met.