Implement RFC-028 stable schema identity

[aaltshuler]

Summary

• activate SchemaIR v2 with a durable graph identity domain plus stable type, property, and table-incarnation IDs
• key manifest authority, OCC, recovery v9, branch merge, maintenance, repair, diffs, and runtime caches by immutable table identity
• preserve identity and physical history across explicit renames while isolating drop/re-add lifetimes with new IDs and paths
• add strict rename validation, historical type-alias binding, real v0.8.1 export/rebuild coverage, and aligned RFC/developer/user documentation

Architecture

This completes the broad RFC-028 slice without introducing a parallel identity registry. Accepted SchemaIR remains the identity authority, Lance remains the physical substrate, and the manifest remains the sole graph visibility boundary. Identity-less older formats are intentionally refused and upgraded through export/init/load rebuild.

Validation

• cargo test --workspace --locked
• cargo test -p omnigraph-engine --features failpoints --test failpoints --locked (119 passed)
• cargo test -p omnigraph-compiler --locked (276 passed)
• scripts/check-agents-md.sh
• git diff --check
• independent blocker review found no actionable issues

Greptile Summary

This PR adds stable schema identity across the compiler, manifest, recovery, and runtime paths. The main changes are:

• SchemaIR v2 with graph-domain type, property, and table-incarnation IDs.
• Manifest schema v5 keyed by immutable table identity instead of public aliases.
• Identity-bearing recovery, schema apply, branch merge, maintenance, repair, diff, and cache paths.
• Upgrade tests and documentation for the new storage identity model.

Confidence Score: 4/5

The stable identity paths need fixes before merging.

• Branch merge can publish without fencing a candidate when alias lookup fails.
• Interface renames can mint a new identity instead of preserving the accepted interface lifetime.
• The manifest, recovery, cache, and staging changes otherwise use identity-keyed state consistently in the inspected paths.

crates/omnigraph/src/exec/merge.rs; crates/omnigraph-compiler/src/catalog/schema_ir.rs; crates/omnigraph-compiler/src/catalog/schema_shape.rs

Important Files Changed

Filename	Overview
crates/omnigraph-compiler/src/catalog/schema_ir.rs	Adds SchemaIR v2 identity allocation and evolution; interface rename binding is missing from the type-shape path.
crates/omnigraph-compiler/src/catalog/schema_shape.rs	Adds canonical schema shapes with rename hints for nodes, edges, and properties.
crates/omnigraph/src/db/manifest/publisher.rs	Moves manifest publication state and preconditions to identity-keyed table maps.
crates/omnigraph/src/db/manifest/recovery.rs	Extends recovery sidecars, pins, effects, and validation with table identity.
crates/omnigraph/src/exec/merge.rs	Adds identity checks to branch merge, but one expected-version bridge can drop unresolved candidates.
crates/omnigraph/src/exec/staging.rs	Carries table identity through staged writes, recovery sidecars, and publish preconditions.
crates/omnigraph/src/runtime_cache.rs	Adds table identity to graph index cache keys to split reincarnated table lifetimes.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
  Source[.pg schema source] --> Shape[SchemaShape]
  Shape --> IR[SchemaIR v2 stable IDs]
  IR --> Catalog[Bound catalog]
  Catalog --> Manifest[Manifest v5 identity rows]
  Manifest --> Paths[Identity-derived Lance paths]
  Manifest --> Recovery[Recovery v9 identity pins]
  Manifest --> Runtime[Diffs, merge, repair, caches]
  Recovery --> Manifest
  Runtime --> Manifest

Loading

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flowchart TD
  Source[.pg schema source] --> Shape[SchemaShape]
  Shape --> IR[SchemaIR v2 stable IDs]
  IR --> Catalog[Bound catalog]
  Catalog --> Manifest[Manifest v5 identity rows]
  Manifest --> Paths[Identity-derived Lance paths]
  Manifest --> Recovery[Recovery v9 identity pins]
  Manifest --> Runtime[Diffs, merge, repair, caches]
  Recovery --> Manifest
  Runtime --> Manifest

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_{Reviews (1): Last reviewed commit: "docs: finalize stable identity contract" | Re-trigger Greptile}

Greptile also left 2 inline comments on this PR.

Context used:

• Context used - AGENTS.md (source)
• Context used - CLAUDE.md (source)