Checkpoints v2: Fix migration rerun logic (speedups, avoid duplicated migration efforts)

[computermode]

https://entire.io/gh/entireio/cli/trails/292

Summary

Fixes a few issues that arose when rerunning `entire migrate --checkpoints v2:

• rerunning the migration could duplicate /full/<n> archives on supposed no-ops (one of our repos grew from gen 46 -> 86),
• interrupting a migration could result in a partially completed state that re-running may not fix properly
• rerunning the migration resulted in an unconditional transcript walk across all the trees every time, even if there was nothing else to be done.

For repos with thousands of checkpoints, the issues above meant that migrations would take 20+ minutes to run even if there was nothing to be done.

Changes

• skip when every session has /full artifacts, pack only the missing sessions when some are absent, fresh-migrate when the checkpoint isn't in /main yet, --force to redo from scratch
• generation-metadata repair only runs when the loop packed something, and just-packed archives are excluded since the packer writes correct generation.json in-memory. A new BuildFullSessionArtifactsIndex turns per-session presence checks into O(1) map lookups, and ReadSessionMetadata reads only metadata.json
• no-op migration reruns now take seconds to run

---

Note

Medium Risk
Touches checkpoint migration and generation repair flows, changing when archives are created and when metadata repair runs; mistakes could skip needed packing or leave inconsistent /full/* state. Scope is contained to migration/repair tooling, but impacts large repos and historical data layout.

Overview
Improves entire migrate --checkpoints v2 rerun behavior so already-migrated checkpoints are skipped when /full/* artifacts are present, while partially migrated checkpoints (written to /main but missing /full/*) resume by packing only missing sessions instead of re-migrating everything.

Speeds up the migration hot path by prebuilding a BuildFullSessionArtifactsIndex for O(1) per-session /full/* presence checks, adding a lightweight ReadSessionMetadata (metadata-only) read, and computing generation.json timestamps from already-loaded transcripts via AggregateTranscriptTimestamps.

Reduces post-migration overhead by running RepairV2GenerationMetadata only when new /full/<n> refs were written, and adds ExcludeRefs support so freshly packed generations are not re-walked during repair. Removes legacy v1 transcript cleanup and compact-transcript backfill/fast-path logic from the migration rerun flow, with tests updated to lock in the new idempotent/resume semantics.

^{Reviewed by Cursor Bugbot for commit 4b333b0. Configure here.}

[Copilot]

Pull request overview

Refines the hidden entire migrate --checkpoints v2 flow so reruns avoid redundant work in the checkpoints-v2 migration pipeline. The PR mainly speeds up reruns by indexing existing /full/* artifacts, repairing only missing packed state, and reducing post-migration generation-metadata work.

Changes:

• Adds a /full/* presence index plus lighter metadata reads to make rerun checks cheaper.
• Reworks rerun behavior to resume interrupted /main→/full packing and skip already-packed checkpoints.
• Avoids recomputing generation metadata for freshly packed refs and limits when the archived-generation repair pass runs.

Reviewed changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
cmd/entire/cli/strategy/generation_repair.go	Adds repair options so callers can exclude freshly written archived refs.
cmd/entire/cli/strategy/generation_repair_test.go	Tests the new exclude-refs repair behavior.
cmd/entire/cli/migrate.go	Reworks migration rerun logic, adds /full indexing, and changes when repair runs.
cmd/entire/cli/migrate_test.go	Updates migration tests around interrupted reruns, no-op reruns, and new checkpoint pickup.
cmd/entire/cli/checkpoint/v2_store_test.go	Replaces legacy cleanup tests with index-behavior tests.
cmd/entire/cli/checkpoint/v2_read.go	Adds a metadata-only v2 read path for hot loops.
cmd/entire/cli/checkpoint/v2_generation.go	Adds in-memory transcript timestamp aggregation for packed generations.
cmd/entire/cli/checkpoint/v2_committed.go	Implements the /full artifact index used by migration reruns.