Restore checkpoints v1 as source of truth

[pfleidi]

https://entire.io/gh/entireio/cli/trails/442

What

• Restores committed checkpoint reads, resume, explain, export, and related workflows to entire/checkpoints/v1.
• Removes checkpoint v2 reader/store/migration/settings/fetch/reconcile paths and tests.
• Keeps the transcript compact package for the next v1 iteration.

How

• Replaces dual-reader paths with direct v1 GitStore reads.
• Deletes v2 stores, resolvers, fixtures, migrate command, and v2 push/fetch/reconcile behavior.
• Updates tests and docs around explain, resume, dispatch, cleanup, settings, doctor, and checkpoint remotes.

Verification

• mise run build
• mise run lint
• mise run test:ci:core
• mise run test:integration
• mise run test:e2e:canary TestDoctorNoIssues
• go test ./cmd/entire/cli -run 'Test(Explain|Resume)'
• mise run lint

---

Note

High Risk
Large removal across checkpoint storage, explain/resume/export, and fetch paths; wrong v1 assumptions could break reading older repos that relied on v2-only data until re-migrated.

Overview
This PR rolls back checkpoints v2 and makes v1 (entire/checkpoints/v1 via GitStore) the only committed checkpoint backend for reads, writes, explain, resume, dispatch, and status.

The large deletion in checkpoint removes NewCommittedReader, DualCheckpointReader, V2GitStore, v2 read/resolve helpers, and their fixtures/tests. Explain and export no longer prefer v2 /main or compact transcripts: they open GitStore directly, prefetch only v1 blobs, and stream stored JSONL for --transcript / --raw-transcript. Git fetch drops v2 ref helpers (FetchV2Main*, checkpoint-remote v2 fetch); tests and docs no longer mention migrate or v2 settings.

Help text and comments are updated so v1 is described as the checkpoint store; migration-era dual-read behavior is gone.

^{Reviewed by Cursor Bugbot for commit 8377a19. Configure here.}

[Copilot]

Pull request overview

This PR removes checkpoints v2 runtime and test paths and restores entire/checkpoints/v1 (checkpoint.GitStore) as the sole committed-checkpoint source of truth for explain/resume/export/list and related workflows across the CLI.

Changes:

• Replaces version-aware/dual committed-checkpoint readers with direct checkpoint.NewGitStore(repo) usage (with blob fetcher wiring where needed).
• Removes checkpoints v2 refs/constants, v2 store/resolve/read implementations, v2 fixtures/tests, and the hidden migrate command.
• Updates tests and help/docs to reflect v1-only committed checkpoint behavior (including transcript export semantics).

Reviewed changes

Copilot reviewed 50 out of 50 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
e2e/tests/doctor_test.go	Drops assertions related to removed v2 doctor output.
cmd/entire/cli/v2_checkpoint_fixture_test.go	Deletes CLI-level v2 checkpoint fixture helpers.
cmd/entire/cli/strategy/v2_checkpoint_fixture_test.go	Deletes strategy-level v2 checkpoint fixture helpers.
cmd/entire/cli/strategy/session.go	Removes v2 fallback when deriving checkpoint descriptions.
cmd/entire/cli/strategy/session_test.go	Removes tests covering v1→v2 description fallback.
cmd/entire/cli/strategy/push_common_test.go	Removes tests for v2-settings push-time warnings.
cmd/entire/cli/strategy/metadata_reconcile.go	Deletes v2 ref disconnection/repair helpers used by doctor/reconcile.
cmd/entire/cli/strategy/manual_commit.go	Removes committed-reader factory method; keeps v1 GitStore accessor.
cmd/entire/cli/strategy/manual_commit_test.go	Removes tests asserting v2-local listing behavior.
cmd/entire/cli/strategy/manual_commit_rewind.go	Switches RestoreLogsOnly to use v1 GitStore directly (with metadata warning).
cmd/entire/cli/strategy/manual_commit_push.go	Removes v2-settings warning call in pre-push flow.
cmd/entire/cli/strategy/manual_commit_condensation.go	Switches list/log reads to v1 GitStore directly (with metadata warning).
cmd/entire/cli/strategy/common.go	Removes v2 fetch tmp ref constant and switches listing to v1 GitStore.
cmd/entire/cli/strategy/checkpoint_remote.go	Removes URL-based v2 /main fetch helper.
cmd/entire/cli/strategy/checkpoint_remote_test.go	Removes tests for v2 URL fetch behavior.
cmd/entire/cli/settings/settings.go	Removes checkpoints v2 settings parsing and warning helpers.
cmd/entire/cli/settings/settings_test.go	Updates tests to focus on non-v2 settings behavior; removes v2-related tests.
cmd/entire/cli/root.go	Unregisters the hidden migrate command.
cmd/entire/cli/rewind.go	Uses v1 GitStore for committed transcript restore.
cmd/entire/cli/review_helpers.go	Uses v1 GitStore for “head has review checkpoint” checks.
cmd/entire/cli/review_context.go	Uses v1 GitStore for building review context from committed checkpoints.
cmd/entire/cli/resume.go	Switches resume committed reads to v1 GitStore and removes v2 metadata fetch path.
cmd/entire/cli/resume_test.go	Updates tests to assert v1-only resolution/transcript behavior.
cmd/entire/cli/paths/paths.go	Removes v2 ref constants and compact/v2 transcript filename constants.
cmd/entire/cli/migrate.go	Deletes deprecated hidden migrate command stub.
cmd/entire/cli/migrate_test.go	Deletes tests for the removed migrate command.
cmd/entire/cli/integration_test/v2_resume_test.go	Deletes integration tests specifically covering v2 resume modes/fallbacks.
cmd/entire/cli/integration_test/testenv.go	Generalizes ref-reading comment (no longer v2-specific).
cmd/entire/cli/integration_test/explain_test.go	Removes v2-mode matrix and v2 treeless assertions; keeps v1 treeless coverage.
cmd/entire/cli/git_operations.go	Removes origin/checkpoint-remote v2 fetch helpers.
cmd/entire/cli/fetch_no_config_pollution_test.go	Removes v2 fetch cases and v2 shallow-repo regression test.
cmd/entire/cli/explain.go	Uses v1 GitStore directly for explain read/list/generate; removes v2 content preference logic.
cmd/entire/cli/explain_test.go	Removes v2-only explain tests and updates remaining tests to v1-only expectations.
cmd/entire/cli/explain_export.go	Removes v2 metadata fetch heuristics and compact transcript streaming; streams stored v1 transcript bytes.
cmd/entire/cli/explain_export_test.go	Reworks export fixtures to write v1 committed checkpoints via GitStore.
cmd/entire/cli/dispatch/mode_local.go	Uses v1 GitStore for candidate enumeration (no version-aware reader).
cmd/entire/cli/dispatch/mode_local_test.go	Updates settings fixture to non-v2 keys consistent with v1-only behavior.
cmd/entire/cli/clean_test.go	Removes v2 help-text expectation.
cmd/entire/cli/checkpoint/v2_store.go	Deletes v2 store implementation.
cmd/entire/cli/checkpoint/v2_store_test.go	Deletes v2 store tests.
cmd/entire/cli/checkpoint/v2_resolve.go	Deletes v2 metadata tree resolver.
cmd/entire/cli/checkpoint/v2_resolve_test.go	Deletes v2 resolver tests.
cmd/entire/cli/checkpoint/v2_read.go	Deletes v2 read paths (main/full refs, archived refs, compact transcript).
cmd/entire/cli/checkpoint/v2_read_test.go	Deletes v2 read-path tests.
cmd/entire/cli/checkpoint/v2_fixture_test.go	Deletes v2 checkpoint fixture utilities in checkpoint package.
cmd/entire/cli/checkpoint/committed_reader_resolve.go	Removes dual-reader factory and v2 interfaces; keeps v1 reader interfaces + helpers.
cmd/entire/cli/checkpoint/committed_reader_resolve_test.go	Replaces dual-reader tests with v1-focused normalization and latest-session transcript tests.
cmd/entire/cli/checkpoint/checkpoint.go	Updates v1 committed-write comment to remove v2 migration reference.
cmd/entire/cli/attach.go	Removes migrate from logging-close comment list.
CLAUDE.md	Updates hidden command inventory to remove migrate.

[pfleidi]

Bugbot run

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^{Reviewed by Cursor Bugbot for commit 8377a19. Configure here.}

[Copilot]

Pull request overview

Copilot reviewed 52 out of 52 changed files in this pull request and generated no new comments.