[codex] Refactor checkpointing Effect services

[juliusmarminge]

Summary

• move the canonical CheckpointDiffQuery and CheckpointStore service modules and their existing tests to the checkpointing domain root
• inline service interfaces and use Service["Service"] for implementation and test-double types
• export each module's concrete make value and module-level layer, with namespace imports in the in-scope consumers
• preserve existing module, service-contract, checkpoint-behavior, and error documentation, and remove the moved test’s stale lint baseline
• delete the two legacy CheckpointStore compatibility shims and migrate orchestration and integration-harness consumers to the canonical namespace

Why

Checkpointing still used split Services/ and Layers/ modules with standalone *Shape interfaces. The domain-root modules now match the repository's target Effect service layout. The requirement is an exported layer; Layer.effect is used here because both make values are genuinely effectful, not to force a constructor pattern.

The follow-up migration includes the checkpoint reactor, its tests, and the integration harness so no compatibility import paths remain. Other orchestration and MCP service modules remain out of scope for this refactor.

Compatibility

• checkpointing/Layers/CheckpointStore.ts and checkpointing/Services/CheckpointStore.ts are deleted
• every consumer imports the canonical root module as * as CheckpointStore and uses CheckpointStore.CheckpointStore / CheckpointStore.layer
• the obsolete CheckpointDiffQuery service path remains removed without a shim

Impact

This is a structural refactor. Checkpoint capture, restore, and diff behavior is unchanged. No test cases or assertions were added; the moved CheckpointDiffQuery test uses @effect/vitest because its canonical root path is covered by the repository's no-manual-Effect-runtime lint rule.

The existing checkpoint errors remain schema-backed structured errors with messages derived from their attributes.

Validation

• focused checkpoint/server/integration/lint-rule test run — 6 files, 143 tests passed and 1 skipped
• vp check — passed with 0 errors; 20 pre-existing warnings remain
• vp run typecheck — all 15 workspace tasks passed
• git diff --check origin/main — passed
• canonical audit — 0 standalone *Shape contracts, 2/2 concrete make exports, 2/2 layer exports, and no redundant Effect.succeed wrappers
• compatibility audit — 0 legacy CheckpointStore paths or CheckpointStoreLive references; 4/4 consumers use the canonical namespace
• test inventory audit — declarations remain exactly 5/3/98 for the moved diff/store tests and server.test.ts (106 before and after)

Note

Refactor checkpointing services to co-locate tags, implementations, and layers

• Consolidates CheckpointStore and CheckpointDiffQuery from separate Services/ and Layers/ files into single modules at CheckpointStore.ts and CheckpointDiffQuery.ts.
• Converts both from interface-based service shapes to Context.Service classes, exporting layer instead of CheckpointStoreLive/CheckpointDiffQueryLive.
• Updates all consumers (orchestration, server wiring, tests, and docs) to use the new namespaced import pattern (* as CheckpointStore) and CheckpointStore.layer.
• Deletes the now-redundant Services/CheckpointStore.ts, Services/CheckpointDiffQuery.ts, and Layers/CheckpointStore.ts files.
• Adds a new test suite for CheckpointDiffQuery covering full-thread diffs, canonical turn-0 refs, whitespace handling, and missing-thread failure cases.

^{Macroscope summarized 8be2b32.}

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Note

Low Risk
Structural import and module-layout refactor only; checkpoint logic is moved and re-exported without intentional behavior changes, with existing tests preserved.

Overview
Checkpointing is reorganized to match the repo’s target Effect layout: CheckpointStore and CheckpointDiffQuery now live as single modules under checkpointing/ with the service tag, implementation (make), and layer colocated. Standalone *Shape interfaces are dropped in favor of Service["Service"] typing.

The old split under checkpointing/Services/ and checkpointing/Layers/ (including CheckpointStoreLive and separate diff-query layer files) is removed with no compatibility shims. Wiring in server.ts, ws.ts, CheckpointReactor, the integration harness, and related tests now uses import * as CheckpointStore / CheckpointDiffQuery and CheckpointStore.layer / CheckpointDiffQuery.layer.

CheckpointDiffQuery.test.ts moves to the domain root and runs via @effect/vitest (replacing manual Effect.runPromise in the deleted Layers test). Docs and the oxlint legacy baseline are updated for the new paths. Runtime behavior for capture, restore, and diff is unchanged.

^{Reviewed by Cursor Bugbot for commit 8be2b32. Bugbot is set up for automated code reviews on this repo. Configure here.}

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