V2 checkpoints migration performance improvements

[computermode]

https://entire.io/gh/entireio/cli/trails/321

Summary

Tested with a repo with ~2500 checkpoints. Reduced migration time to ~3.5 minutes (migrate_checkpoints 216869ms), down from ~5.5 minutes (migrate_checkpoints 337738ms).

Validated with a fresh migration of the repo locally and compared with the version pushed up to GH, ensured there were no regressions in the data pushed up. See the comparison report here: https://gist.github.com/computermode/1c06c434317fb8fe7df18b4598913ab8

Script to compare repos: https://gist.github.com/computermode/599fea82d7ae0147716997de8f19576a

Biggest Redundancies

Area	Before	After
Raw transcript packing	Re-chunked and re-stored v1 transcript blobs into v2	Reuses existing v1 blob hashes
Generation metadata	Rescanned raw transcripts for timestamps	Uses already-loaded checkpoint CreatedAt first
Compact offsets	Compacted full transcript, then compacted scoped suffix again	Caches raw-position -> compact-line offset
/main flush	Repeated tree surgery per checkpoint inside each batch	Builds subtrees, applies root changes once
V2 existence checks	Read v2 summary per checkpoint	Builds one v2 presence index

Where It Showed Up In Trace

• pack_full_generation_total: duplicate raw transcript packing
• pack_full.generation_timestamps_total: raw transcript timestamp rescans
• migrate_one.compact_transcript_total: duplicate compact passes
• flush_main_total: repeated /main tree rewrites
• per-checkpoint migration overhead: repeated v2 summary lookups

Key Point

The batch size was already 100; the slowdown was inside each batch from repeated blob work, transcript parsing, and Git tree rewrites.

---

Note

Medium Risk
Touches checkpoint migration and v2 git ref-writing logic; while covered by new invariants/tests, mistakes could lead to missing or mis-indexed checkpoint data during migration.

Overview
Speeds up v1→v2 checkpoint migration by batching v2 /main writes: migration now buffers per-session WriteCommittedOptions and flushes them via a new WriteCommittedMainBatch that updates /main with a single commit/CAS per batch.

Avoids redundant work during /full/* packing by reusing existing v1 transcript blob hashes (surfaced via SessionContent.TranscriptBlobHashes) and by preferring checkpoint CreatedAt when generating generation.json, falling back to transcript timestamp scans only when needed.

Adds a compact-transcript offset cache and cumulative perf annotation (perf.Annotate) to reduce repeated offset computation and make phase totals visible, alongside new tests validating batch-vs-sequential tree equality, single-commit behavior, and raw-blob reuse.

^{Reviewed by Cursor Bugbot for commit 961c195. Configure here.}

[Copilot]

Pull request overview

This PR targets faster v1→v2 checkpoint migration in the Entire CLI by eliminating repeated blob/transcript work and reducing repeated /main tree rewrites during migration.

Changes:

• Adds perf.Annotate to surface cumulative (summed) timings in perf traces without per-iteration spans.
• Speeds migration by batching /main writes (WriteCommittedMainBatch), reusing v1 transcript blob hashes when packing v2 /full/*, and caching compact-transcript offset calculations.
• Adjusts generation metadata packing to prefer already-loaded checkpoint CreatedAt instead of rescanning raw transcripts, with corresponding test updates.

Reviewed changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
perf/span.go	Adds Annotate for synthetic child spans with precomputed duration.
perf/span_test.go	Adds tests for Annotate behavior (duration + no-parent no-op).
cmd/entire/cli/migrate.go	Refactors migration loop for batching, caching, and reduced redundant work; adds perf aggregation annotations.
cmd/entire/cli/migrate_test.go	Adds coverage for raw blob reuse and updates migration-related expectations.
cmd/entire/cli/checkpoint/v2_store_test.go	Adds correctness + perf invariants tests for WriteCommittedMainBatch.
cmd/entire/cli/checkpoint/v2_committed.go	Introduces WriteCommittedMainBatch and supporting subtree-building helpers.
cmd/entire/cli/checkpoint/committed.go	Captures v1 transcript blob hashes during session reads for reuse during migration.
cmd/entire/cli/checkpoint/checkpoint.go	Extends SessionContent with TranscriptBlobHashes to support blob reuse.