feat: v2 dual-write for checkpoints behind feature flag

[pfleidi]

Summary

Introduces checkpoints v2 dual-write support. When checkpoints_v2 is enabled in strategy options, the CLI writes checkpoint data to both v1 (entire/checkpoints/v1 branch) and v2 custom refs (refs/entire/checkpoints/v2/main and refs/entire/checkpoints/v2/full/current).

• V2GitStore — new store type for v2 ref operations, separate from GitStore (v1) to simplify future v1 removal
• /main ref — receives metadata, prompts, session metadata (no raw transcript or content hash). Compact transcript.jsonl will be added here once compaction (workstream B) is ready
• /full/current ref — accumulates raw transcripts (full.jsonl) + content_hash.txt across checkpoints via tree splicing (same pattern as v1). Generation rotation will archive and reset this ref when it reaches capacity (future work)
• Dual-write wiring — CondenseSession and stop-time finalization both dual-write, gated by settings.IsCheckpointsV2Enabled(). V2 failures are best-effort (logged as warnings, never block v1)
• Stop-time optimization — v2 feature flag is evaluated once before the finalization loop (not per-checkpoint) to avoid repeated settings I/O

What's NOT in scope (future steps per design spec)

• Task checkpoint support on /main
• Push logic for v2 refs
• Read paths (entire status, entire explain, entire resume)
• Generation rotation for /full/current
• Compact transcript format / compaction (workstream B)
• v1 → v2 migration tool

Test plan

• 20 unit tests for V2GitStore (ref management, write/update for both refs, multi-session, accumulation, edge cases)
• 2 strategy-level tests (v2 enabled vs disabled in CondenseSession)
• 3 integration tests (full workflow, disabled path, stop-time finalization)
• mise run fmt && mise run lint — 0 issues
• mise run test:ci — all unit, integration, and E2E canary tests pass

🤖 Generated with Claude Code

[Copilot]

Pull request overview

Adds a feature-flagged “checkpoints v2” dual-write path so the manual-commit strategy can persist checkpoint data to both the existing v1 metadata branch and the new v2 custom refs, enabling a gradual migration without breaking current read paths.

Changes:

• Wire dual-write into CondenseSession and stop-time finalization (UpdateCommitted) behind settings.IsCheckpointsV2Enabled(), with v2 failures treated as best-effort.
• Introduce V2GitStore to write v2 checkpoint data to custom refs (/main for metadata/prompts, /full/current for raw transcript + content hash).
• Add unit + strategy-level + integration tests, and extend integration TestEnv helpers to read from arbitrary refs.

Reviewed changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
cmd/entire/cli/strategy/manual_commit_condensation.go	Builds shared v1/v2 write opts and adds best-effort v2 dual-write during condensation.
cmd/entire/cli/strategy/manual_commit_hooks.go	Adds best-effort v2 dual-write during stop-time checkpoint finalization.
cmd/entire/cli/strategy/manual_commit_test.go	Adds strategy-level tests for v2 dual-write enabled/disabled behavior.
cmd/entire/cli/paths/paths.go	Defines v2 custom ref names under refs/entire/....
cmd/entire/cli/integration_test/v2_dual_write_test.go	Adds integration coverage for full workflow, disabled path, and stop-time finalization.
cmd/entire/cli/integration_test/testenv.go	Adds helpers for reading files from full refs and for checking ref existence.
cmd/entire/cli/checkpoint/v2_store.go	Adds low-level v2 ref creation/state/update primitives.
cmd/entire/cli/checkpoint/v2_committed.go	Implements v2 committed write/update logic for /main and /full/current.
cmd/entire/cli/checkpoint/v2_store_test.go	Adds unit tests for v2 ref management and committed write/update behavior.
cmd/entire/cli/checkpoint/committed.go	Reuses shared write-option validation via validateWriteOpts.
cmd/entire/cli/checkpoint/checkpoint.go	Makes SessionFilePaths JSON fields omitempty to support v2 layouts with missing fields.

[Copilot]

Pull request overview

Copilot reviewed 10 out of 10 changed files in this pull request and generated 4 comments.

[computermode]

We chatted about these changes together, approving to unblock testing/progress. Thank you for thinking through the updated ref changes and talking through them with me. 😄

Since GH swallowed my comments and I can't seem to undo that, I'll echo here that I think creating packages for v1 vs v2 might be a nice way to approach changes like this in the future.

[Soph]

otherwise 👍