Implemented Crate Layout

Module layout for the reference crate:

dtcs/
  Cargo.toml
  SPEC.md              # repository root — authoritative spec
  docs/
    editorial/         # specification authoring process
    implementation/    # this guide set
  examples/
  tests/
  src/
    lib.rs
    model/
      mod.rs
      contract.rs
      metadata.rs
      interface.rs
      types.rs
      semantics.rs
      expression.rs
      action.rs
      function.rs
      rule.rs
      lineage.rs
      guarantees.rs
      compatibility_decl.rs
      null_behavior.rs
      versioning.rs
      extension.rs
      registry.rs
    parser/
      mod.rs
      yaml.rs
      json.rs
    validation/
      mod.rs
      phases.rs
      field_index.rs
      lineage.rs
      structural.rs
      interfaces.rs
      types.rs
      references.rs
      semantics.rs
      extensions.rs
    metadata/
      mod.rs
      validate.rs
    diagnostics/
      mod.rs
      codes.rs
      diagnostic.rs
      severity.rs
      category.rs
      stage.rs
      report.rs
    compatibility/
      mod.rs
      types.rs
      report.rs
      compare.rs
      classify.rs
      evolution.rs
    versioning/
      mod.rs
      validate.rs
    lineage/
      mod.rs
      analysis.rs
    analysis/
      mod.rs
      contract.rs
      semantics.rs
      expr/
        mod.rs
        ast.rs
        parse.rs
        types.rs
        constants.rs
        rewrite.rs
    registry/
      mod.rs
      builtin.rs
      load.rs
      cache.rs
    plan/
      mod.rs
      model.rs
      lowering.rs
      graph.rs
      validate.rs
      optimize.rs
      equivalence.rs
      rule_key.rs
      portable.rs          # Phase 0.12 portable transform-plan export
    capability/
      mod.rs
      model.rs
      builtin.rs
      requirements.rs
      match.rs
      validate.rs
      portable.rs          # Phase 0.12 capability accuracy / manifests
    compile/
      mod.rs
      model.rs
      compiler.rs
      reference.rs
      validate.rs
    runtime/
      mod.rs
      model.rs
      actions.rs
      functions.rs
      rules.rs
      expr.rs
      lineage.rs
      reference.rs
      validate.rs
      runtime_trait.rs
    conformance/
      mod.rs
      profiles.rs
      runner.rs
      model.rs
      security.rs
      portable.rs          # Phase 0.12 portableDifferential runner
      manifest.json
    cli/
      mod.rs
    bin/
      dtcs.rs
  python/
    dtcs/
  tests/
    fixtures/
      compatibility/
      runtime/
      capability/
      portable/            # Phase 0.12 differential fixtures
      plans/
      plans_optimized/
      execution_plans/
    conformance/
      manifest.json
    fixture_expectations.json
    plan_expectations.json
    optimize_expectations.json
    mvp.rs
    phase_0_2.rs
    phase_0_3.rs
    phase_0_4.rs
    phase_0_6.rs
    phase_0_7.rs
    phase_0_8.rs
    phase_0_9.rs
    phase_0_10.rs
    phase_0_11.rs
    portable_relational.rs
    manifest.rs

Keep modules small and aligned with SPEC.md.