Remove checkpoints v1.1 mirror machinery

[pfleidi]

https://entire.io/gh/entireio/cli/trails/597

Why

The checkpoints v1.1 rollout is no longer moving forward. Keeping the custom-ref read mirror, checkpoints_version setting, and mirror repair paths would preserve a second checkpoint topology that conflicts with the newer checkpoint-store abstraction direction from #1433.

What changed

Committed checkpoint metadata now resolves to entire/checkpoints/v1 only. The retired v1.1 mirror maintenance, pre-push mirroring, doctor/bundle diagnosis, settings parsing, tests, and active architecture docs were removed.

Implementation decisions

This keeps the checkpoint.Open construction seam from #1451, but trims no-op settings and stale facade surface after the committed refs were collapsed to v1. No fallback reads or migration from refs/entire/checkpoints/v1.1 were added; existing v1.1 refs become inert git data.

Tradeoffs and alternatives considered

We removed strategy_options.checkpoints_version instead of leaving it as a compatibility no-op because the option was never public or active. Keeping it would invite future code to preserve the retired v1.1 topology.

Reviewer notes

Published changelog entries are intentionally left unchanged.

---

Note

Medium Risk
Wide changes to committed-metadata read/write, push, fetch, resume, and doctor paths; wrong ref handling could hide checkpoints until users fetch v1, though behavior is intentionally unified on a single topology.

Overview
Removes the retired checkpoints v1.1 path: committed metadata no longer uses a separate read mirror (refs/entire/checkpoints/v1.1), strategy_options.checkpoints_version, or settings-driven ref topology. ResolveCommittedRefs always returns the v1-only CommittedRefs (Primary, Read, and Push all on entire/checkpoints/v1).

The strategy/v1_custom_ref_mirror layer is deleted—no post-write mirroring, pre-push mirror refresh, fetch-time mirror updates, or AdvanceCommittedPrimary mirror side effects. Ref updates go through direct setRefHash on the v1 branch. entire doctor no longer diagnoses or repairs mirror drift; diagnostic bundles drop mirror status lines.

checkpoint.Open is simplified (no settings-based ref resolution; Temporary() aliases Primary). Call sites such as attach, explain summary save, and git metadata fetch stop calling mirror helpers. paths.MetadataRefName and MirrorsToV1CustomRef are removed. Architecture docs and large v1.1-specific test suites are removed or rewritten for v1-only behavior.

Unrelated: ParseGitHubRemote now delegates to gitremote.ParseURL (including Entire mirror remotes). Minor go.mod bumps (ogen, goldmark). Existing local v1.1 refs are not migrated—they become inert git refs.

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[pfleidi]

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[Copilot]

Pull request overview

This PR removes the checkpoints v1.1 “custom ref” mirror topology and associated maintenance/diagnostics paths, returning committed checkpoint reads/writes/pushes to a single v1 ref (entire/checkpoints/v1). This aligns the codebase with the newer checkpoint-store abstraction direction by dropping the unused/refuted alternate topology and its settings surface.

Changes:

• Remove v1.1 mirror machinery across strategy, hooks, push/fetch/reconcile, doctor/bundle, and tests; committed metadata resolves to v1 only.
• Simplify checkpoint ref topology resolution and checkpoint.Open options to default to v1, ignoring the retired strategy_options.checkpoints_version.
• Update documentation/tests accordingly; adjust GitHub remote parsing to delegate to gitremote.ParseURL (including Entire mirror remotes) and add validation for extra path segments.

Reviewed changes

Copilot reviewed 48 out of 49 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
go.sum	Bump dependency checksums (ogen, goldmark).
go.mod	Bump ogen and goldmark versions.
docs/architecture/sessions-and-checkpoints.md	Remove v1.1 mirror documentation; document v1-only committed storage.
cmd/entire/cli/strategy/v1_custom_ref_mirror.go	Delete v1.1 mirror implementation.
cmd/entire/cli/strategy/v1_custom_ref_mirror_test.go	Delete v1.1 mirror unit tests.
cmd/entire/cli/strategy/rewind_test.go	Remove v1.1 transcript read-path test coverage.
cmd/entire/cli/strategy/push_common.go	Stop advancing mirror during fetch/rebase ref updates (v1-only).
cmd/entire/cli/strategy/push_common_test.go	Update tests/comments to use a generic non-branch ref example; remove v1.1 expectations.
cmd/entire/cli/strategy/metadata_reconcile.go	Stop advancing mirror during metadata ref reconciliation (v1-only).
cmd/entire/cli/strategy/metadata_reconcile_test.go	Remove reconciliation test asserting v1.1 mirror behavior.
cmd/entire/cli/strategy/manual_commit_test.go	Remove v1.1 committed-read mirror test for rewind-point prompt reads.
cmd/entire/cli/strategy/manual_commit_push.go	Remove pre-push mirror refresh behavior.
cmd/entire/cli/strategy/manual_commit_hooks.go	Remove best-effort mirror updates after committed writes in hooks.
cmd/entire/cli/strategy/manual_commit_condensation.go	Remove best-effort mirror updates after condensation writes.
cmd/entire/cli/strategy/common.go	Replace “advance primary + mirror” with v1-only ref updates in EnsurePrimaryRef.
cmd/entire/cli/strategy/common_test.go	Update EnsurePrimaryRef tests to v1-only behavior.
cmd/entire/cli/strategy/cleanup.go	Update orphan cleanup to advance only v1.
cmd/entire/cli/strategy/clean_test.go	Remove orphan detection test that depended on v1.1 read topology.
cmd/entire/cli/strategy/checkpoint_remote.go	Remove mirror refresh after metadata fetch.
cmd/entire/cli/strategy/checkpoint_remote_test.go	Remove test assertions tied to v1.1 mirroring after fetch.
cmd/entire/cli/settings/settings.go	Remove v1.1 mirror opt-in helpers from settings surface.
cmd/entire/cli/settings/settings_test.go	Remove tests for v1.1 checkpoints_version parsing helpers.
cmd/entire/cli/search/search_test.go	Add tests for Entire mirror remote parsing and extra path segment rejection.
cmd/entire/cli/search/github.go	Delegate remote parsing to gitremote.ParseURL; validate/normalize GitHub remotes incl. Entire mirrors.
cmd/entire/cli/review_context_test.go	Remove v1.1 custom-ref read-path test cases.
cmd/entire/cli/resume.go	Open checkpoint stores via checkpoint.Open and remove v1.1 bootstrap special-casing.
cmd/entire/cli/resume_test.go	Remove resume behavior tests that relied on v1.1 reads/topology.
cmd/entire/cli/paths/paths.go	Remove v1.1 custom ref constant.
cmd/entire/cli/integration_test/remote_operations_test.go	Remove integration coverage for pushing v1.1 mirror ref.
cmd/entire/cli/integration_test/attach_test.go	Remove integration coverage for attach creating/updating v1.1 ref.
cmd/entire/cli/head_checkpoint_flags_test.go	Remove v1.1 custom-ref read-path test coverage.
cmd/entire/cli/git_operations.go	Remove mirror refresh after fetching metadata from origin.
cmd/entire/cli/git_operations_test.go	Remove fetch+mirror v1.1 ref test.
cmd/entire/cli/explain.go	Remove mirror repair after summary write; simplify summary generation call path.
cmd/entire/cli/explain_test.go	Update summary-generation tests to v1-only behavior.
cmd/entire/cli/doctor.go	Remove doctor check/repair flow for v1.1 read mirror drift.
cmd/entire/cli/doctor_test.go	Remove tests covering v1.1 mirror diagnosis/repair and doctor wiring.
cmd/entire/cli/doctor_bundle.go	Remove mirror diagnosis reporting from bundles; keep refs listing.
cmd/entire/cli/doctor_bundle_test.go	Update bundle expectations to exclude mirror status lines.
cmd/entire/cli/dispatch/mode_local.go	Update comments around repo-scoped store construction (no v1.1 topology).
cmd/entire/cli/dispatch/mode_local_test.go	Remove dispatch tests that relied on v1.1 custom-ref reads.
cmd/entire/cli/checkpoint/store.go	Update GitStore comment to remove mirror advancement mention.
cmd/entire/cli/checkpoint/open.go	Remove settings-based ref resolution; default to v1 and keep explicit ref override.
cmd/entire/cli/checkpoint/committed_refs.go	Collapse CommittedRefs to v1-only and remove mirror fields/topology branching.
cmd/entire/cli/checkpoint/committed_refs_test.go	Update tests to assert checkpoints_version is ignored and v1 refs are used.
cmd/entire/cli/checkpoint/committed_read_store_test.go	Remove v1.1 read-path tests; assert checkpoints_version is ignored.
cmd/entire/cli/attach.go	Remove injected-settings topology override; stop mirroring after committed writes.
cmd/entire/cli/attach_test.go	Remove attach test asserting v1.1 mirror advancement.
CLAUDE.md	Remove v1.1 mirror behavior from architecture notes.

[Soph]

Reviewed the full diff. Behavior-preserving v1.1 removal: the AdvanceCommittedPrimary/AdvanceLocalRef → setRefHash swap drops only the mirror side-effect (correct), checkpoint.Open centralizes ref + blob-fetcher wiring cleanly, and docs (CLAUDE.md + sessions-and-checkpoints.md) are updated in lockstep. Verified locally: go build, go vet, and checkpoint/strategy/settings package tests all green; grepped every removed symbol — no dangling references (only the intentional historical CHANGELOG entry and the TestNewGitStore_IgnoresCheckpointsVersion regression test). Main residual risk (inert local v1.1 refs) is intentional and documented. LGTM.