Add Commander-governed native RNA, DNA, and CLI spine

[FreshSoftware4]

Purpose

Begin the additive Locus64 reimplementation with a smaller semantic core instead of extending the legacy record ontology, and put the cutover sequence under a Commander-native evidence rail.

Native authority added

• one compact node algebra for types, values, operations, judgments, and witnesses
• composed numeric routes with no native names
• ordered 8-byte ports
• persistent context deltas
• one transition journal
• bounded canonical graph decode/re-encode fixed point
• role-separated BLAKE3 commitments
• proof-carrying transactional admission
• compact L64D native DNA
• compact L64R1 authored RNA

Public CLI membrane

The existing command names now route structurally native artifacts directly:

normalize-rna L64R1
compile-rna L64R1 -> L64D
sequence-dna L64D -> canonical L64R1
verify-roundtrip L64R1

No parallel native binary or duplicate command surface was added. The original 1,910-line legacy dispatcher remains unchanged and is included behind the membrane for all other commands.

Native source rejects legacy-only artifact classes and lineage flags. Invalid mathematical operations fail before output creation.

Legacy demotion

Legacy RNA/DNA execution is classified as compatibility/forensic ingress:

l64-cli legacy <old-rna-or-dna-command> ...

Ambient compatibility remains temporarily available for existing workflows but emits a mandatory deprecation warning. Native contacts emit no legacy warning.

Commander rail

LOCUS64_NATIVE_RAIL.athens records and has completed three evidence-gated stages:

1. native-rna-pilot
2. native-cli-membrane
3. legacy-demotion

Each completion records the corresponding successful GitHub workflow run.

Anti-growth boundary

• no native string identities, JSON, bincode, generic authority serialization, or claim/theorem/campaign IDs
• Node <= 32 bytes
• Port <= 8 bytes
• one graph, route index, journal, canonical codec, DNA frame, RNA ingress, and transaction path
• no second CLI executable
• no edits to the legacy dispatcher

Verification

The branch gate passes:

cargo fmt --all --check
cargo test --workspace --all-targets
cargo clippy -p l64-native --all-targets -- -D warnings

Coverage includes valid and invalid mathematical workloads, proof-carrying admission, canonical graph and DNA fixed points, authored RNA normalization, RNA→DNA→RNA→DNA identity, CLI native cutover, legacy fallback preservation, explicit legacy ingress, visible ambient demotion, and warning-free native execution.

Remaining boundary

This is still additive. The legacy runtime, registry, certification stack, and packet implementation remain internally present. Their next replacement must be selected by a new Commander rail rather than extending this completed cutover rail informally.

[FreshSoftware4]

Integration verification is green.

GitHub Actions run 29976633612 completed successfully with:

• cargo fmt --all --check
• cargo test -q across the full workspace
• cargo clippy -p l64-native --all-targets -- -D warnings

The isolated local gate also passed all four first-slice tests. The branch remains intentionally additive; no legacy authority path has been removed or rerouted yet.

[FreshSoftware4]

Superseded by draft PR #3, which carries the same native RNA/DNA/CLI spine plus the completed Commander-governed constraint-core change chain. PR #2's head association became stale during low-level branch promotion, so further development and verification continue only on PR #3.