Prevent pack file race condition during checkpoint sync

[pjbgf]

https://entire.io/gh/entireio/cli/trails/6148e08144d9

Summary

• Disable auto-gc during all fetch operations (--no-auto-gc) to prevent a race condition where git gc repacks/deletes pack files while go-git is reading from them, causing ENOENT errors during checkpoint sync
• Remove shallow checkpoint fetches (--depth=1) — shallow repos break commands that need checkpoint ancestry/history, and the bandwidth savings are now handled by filtered fetches instead
• Auto-unshallow legacy shallow repos — when filtered_fetches is enabled and the repo is shallow (from a previous --depth=1 fetch), the next filtered fetch adds --unshallow to migrate away from shallow state
• Gate tree-only fetch paths on filtered_fetches — FetchMetadataTreeOnly and FetchV2MainTreeOnly only make sense when filtered fetches are enabled (they skip blobs); without the setting, callers fall back to full fetches that include blob content

Context

After enabling filtered_fetches in the project settings, users hit this error during git push:

[entire] Warning: couldn't sync entire/checkpoints/v1: failed to rebase local
commits onto remote: failed to flatten tip tree: failed to get subtree
36/db97269a69: open .git/objects/pack/pack-.pack: no such file or directory

Each filtered fetch creates a promisor pack file. Accumulating promisor packs reaches the gc.autoPackLimit threshold, triggering gc --auto which repacks and deletes old pack files.
go-git snapshots the pack file list when the repository is opened, then fails when it tries to read from a pack that was deleted by gc between the snapshot and the read.

---

Note

Medium Risk
Touches checkpoint sync/fetch behavior and Git plumbing flags, so regressions could impact resume/explain flows or fetch performance across different repo states (shallow vs full). Changes are scoped and covered by an added unshallow migration test.

Overview
Prevents packfile races during checkpoint sync by adding --no-auto-gc to all checkpoint-related git fetch invocations (including blob-by-hash and v2 /full/* fetches), avoiding background repacks while go-git is reading.

Removes legacy shallow checkpoint fetches and, when filtered_fetches is enabled, automatically migrates existing shallow repos by detecting shallow state and adding --unshallow on subsequent filtered fetches.

Adjusts resume/explain metadata fetch fallbacks so the “tree-only” fast path is only used when filtered_fetches is enabled; otherwise callers fall back to full, blob-inclusive fetches. Adds a test ensuring filtered fetches unshallow a legacy shallow clone.

^{Reviewed by Cursor Bugbot for commit 8cb8c82. Configure here.}

[Copilot]

Pull request overview

This PR addresses checkpoint sync failures caused by git gc --auto repacking/deleting pack files while go-git is reading them, by preventing auto-GC during fetches and by improving fetch behavior (removing shallow fetches, migrating legacy shallow repos, and gating tree-only fetch fast paths on filtered_fetches).

Changes:

• Add --no-auto-gc to git fetch operations to prevent packfile races during checkpoint sync.
• Remove shallow checkpoint fetch behavior and add an auto---unshallow migration for legacy shallow repos when filtered_fetches is enabled.
• Only use “tree-only” fetch paths when filtered_fetches is enabled; otherwise fall back to full fetches.

Reviewed changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
cmd/entire/cli/strategy/common.go	Removes outdated comment about --depth=1 compatibility with ancestry checks.
cmd/entire/cli/resume.go	Gates tree-only metadata fetch path on filtered_fetches; adjusts v2 tree-only fetch injection.
cmd/entire/cli/git_operations.go	Removes shallow fetch option plumbing; updates metadata/v2 fetch helpers accordingly.
cmd/entire/cli/explain.go	Uses tree-only vs full fetch depending on filtered_fetches setting.
cmd/entire/cli/checkpoint/v2_read.go	Adds --no-auto-gc to v2 full-ref fetches.
cmd/entire/cli/checkpoint/remote/git.go	Adds --no-auto-gc to fetches; adds shallow-repo detection and --unshallow migration logic.
cmd/entire/cli/checkpoint/remote/git_test.go	Updates tests for new --no-auto-gc argument; adds a test for unshallowing legacy shallow repos.

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