superseded: semantic interoperability foundation design draft

[TheHalfMoon]

Purpose

Establish the initial commandF foundation after the final FHIR/interoperability donor and gap audit.

What this PR adds

• a provenance-controlled donor inventory and adoption policy
• a gap-to-solution architecture for FHIR and cross-standard interoperability
• a separate research agenda under research/
• an initial Rust workspace
• commandf-csir: typed clinical semantic IR primitives and explicit loss events
• commandf-evidence: machine-readable transformation certificate contracts
• CI for format, clippy, and tests

Core architecture decision

FHIR is a first-class commandF dialect and validation target, but it is not the sole internal canonical model. commandF will parse source dialects, preserve facts in a typed semantic IR, compile mappings, lower to target dialects, run authoritative validators/oracles, and emit explicit semantic-loss and transformation evidence.

Donor strategy

Prefer DEPEND, IMPORT, and independent ORACLE use. PORT/COPY are allowed only after exact repository commit, source path, license/permission, notices, and modifications are pinned in donor provenance records.

No unverifiable leaked/proprietary source is eligible for ingestion. Founder-authorized private source can be audited when supplied through an authorized source with permission evidence.

Research separation

Candidate papers and master's research directions are isolated in research/RESEARCH_AGENDA.md; they are not product requirements or clinical claims.

Validation

GitHub Actions will run:

• cargo fmt --all -- --check
• cargo clippy --workspace --all-targets --all-features -- -D warnings
• cargo test --workspace --all-features

This PR is intentionally Draft while the bootstrap contracts and donor pins are reviewed.

---

Summary by cubic

Bootstraps commandF’s semantic interoperability foundation with typed Rust contracts and automated review configs, enabling provenance and compatibility certification before adopting donor code. No runtime adapters ship; behavior change is limited to CI and PR review automation.

• Adds Rust workspace crates: commandf-csir (typed CSIR with loss accounting), commandf-evidence (transformation certificates), commandf-findings (evidence-bearing findings), commandf-package (content-addressed package/lock contracts), commandf-validator (implementation-neutral validator descriptors), commandf-profiler (read-only JSON profiling), commandf-review (breaking-change reports and quality gates).
• Adds foundation docs (master plan, gap→solution map, consumer compatibility matrix, provenance/donor policy, Big Tech deep dive) and donor registries under donors/*.
• Configures CI (.github/workflows/ci.yml) to run fmt, clippy, and workspace tests (Rust 1.75).
• Enables automated PR reviews via .coderabbit.yaml and configures Qodo PR-Agent via .pr_agent.toml; adds engineering rules in AGENTS.md and review best_practices.md.
• Updates README.md with the pipeline and FHIR positioning; adds workspace Cargo.toml and .gitignore.
• Applies rustfmt to commandf-review contracts; no API or behavior changes.

Review and rollout

• Pin all UNPINNED refs in donors/* before any DEPEND/PORT/COPY/IMPORT/ORACLE adoption.
• Treat these crates as compile-time contracts only; no runtime adapters ship in this PR.
• Use Rust 1.75 locally; CI must pass before merge. Automated reviews from CodeRabbit and PR-Agent will run on this branch.

^{Written for commit 15c71e8. Summary will update on new commits.}

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Review details

⚙️ Run configuration

Configuration used: Path: .coderabbit.yaml

Review profile: ASSERTIVE

Plan: Pro Plus

Run ID: 8f327f7b-930e-46e1-8c06-95958127a7d3

📥 Commits

Reviewing files that changed from the base of the PR and between cd7972f and 15c71e8.

📒 Files selected for processing (33)

• .coderabbit.yaml
• .github/workflows/ci.yml
• .gitignore
• .pr_agent.toml
• AGENTS.md
• Cargo.toml
• README.md
• best_practices.md
• crates/commandf-csir/Cargo.toml
• crates/commandf-csir/src/lib.rs
• crates/commandf-evidence/Cargo.toml
• crates/commandf-evidence/src/lib.rs
• crates/commandf-findings/Cargo.toml
• crates/commandf-findings/src/lib.rs
• crates/commandf-package/Cargo.toml
• crates/commandf-package/src/lib.rs
• crates/commandf-profiler/Cargo.toml
• crates/commandf-profiler/src/lib.rs
• crates/commandf-review/Cargo.toml
• crates/commandf-review/src/lib.rs
• crates/commandf-validator/Cargo.toml
• crates/commandf-validator/src/lib.rs
• docs/BIG_TECH_TECHNOLOGY_DEEP_DIVE_2026-08-13.md
• docs/COMMAND_F_CONSUMER_COMPATIBILITY.md
• docs/COMMAND_F_MASTER_PLAN_2026-08-13.md
• docs/DONOR_AUDIT_2026-08-13.md
• docs/GAP_SOLUTION_MAP.md
• docs/PROVENANCE_AND_DONOR_POLICY.md
• donors/big-tech-2026-08-13.yaml
• donors/final-pass-2026-08-13.yaml
• donors/manifest.yaml
• donors/review-quality-2026-08-13.yaml
• research/RESEARCH_AGENDA.md

✨ Finishing Touches 💡 1

🛠️ Fix failing CI checks 💡

• Create stacked PR
• Commit on current branch

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch bootstrap/commandf-foundation

---

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[TheHalfMoon]

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[TheHalfMoon]

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