git_operations: stop shallow-fetching the metadata tip (root-cause fix for shallow-metadata false-disconnect)

[Soph]

https://entire.io/gh/entireio/cli/trails/578

Problem

FetchMetadataTreeOnly resolves the latest checkpoint on resume / explain / attach by fetching the entire/checkpoints/v1 tip with --depth=1. A depth-1 fetch adds the fetched commit to .git/shallow. Once the metadata tip is a shallow boundary, a later git merge-base against refs/remotes/origin/entire/checkpoints/v1 can't reach the real common ancestor (it lives below the boundary), so the disconnection check falsely reports "no common ancestor" — aborting git push and looping entire doctor.

This is the upstream source of the shallow-metadata false-disconnect. It's self-inflicted by the CLI's own tip-read, which runs on essentially every entire resume when checkpoints live on origin (no checkpoint_remote to short-circuit it via getMetadataTree). The user never has to clone shallowly — the CLI shallows the branch for them.

Why not "fetch the tip into a throwaway ref"?

The shallow boundary is intrinsic to --depth=1: it truncates the fetched commit, regardless of which ref it lands on, and git (2.54) opportunistically points refs/remotes/origin/<branch> at that commit anyway (verified against --refmap=, fetch-by-URL, FETCH_HEAD-only, and -c remote.origin.fetch=). You cannot read a tip via --depth=1 without creating a shallow boundary on the shared object store.

Fix

Stop shallow-fetching. FetchMetadataTreeOnly now fetches the metadata commit+tree graph at full depth, relying on --filter=blob:none (when filtered fetches are enabled) to skip blob content instead of on depth-limiting. No shallow boundary is ever created, so refs/remotes/origin/<branch> stays connected and merge-base works.

git fetch is incremental, so after the first fetch only new commits/trees travel — the cheapness now comes from blob filtering + incremental fetch rather than from truncating history.

Test

TestFetchMetadataTreeOnly_DoesNotShallowRepo seeds a 2-commit metadata branch, runs the tip-read on a clone, and asserts the repo is not shallow afterward (--is-shallow-repository=false), full history is present, and the local primary ref is advanced. Under the old --depth=1 behavior the repo would be shallow.

Notes

• Repos with a configured checkpoint_remote were never affected (that path short-circuits before the shallow fetch and is already full-depth).
• Complements the detection-side hardening in strategy: don't treat shallow merge-base miss as disconnected metadata #1434 (IsMetadataDisconnected shallow-awareness + doctor deepen); this PR removes the source so the boundary isn't created in the first place.
• Unit + relevant integration tests (filtered_fetches enabled) pass.

🤖 Generated with Claude Code

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Note

Medium Risk
Changes default fetch behavior on a hot path (resume/explain/attach), which can increase first-fetch work on repos without blob filtering, but fixes incorrect disconnect detection tied to git shallow state.

Overview
FetchMetadataTreeOnly (used on resume/explain/attach to read the latest checkpoint) no longer uses --depth=1. It fetches the metadata branch at full commit/tree depth and stays cheap via --filter=blob:none when filtered fetches are on, instead of truncating history.

That removes the root cause where a depth-1 fetch wrote a shallow boundary and later git merge-base / strategy.IsMetadataDisconnected falsely reported no common ancestor—blocking push and looping entire doctor.

The Shallow option is dropped from fetchMetadataOpts. TestFetchMetadataTreeOnly_DoesNotShallowRepo asserts the clone stays non-shallow, keeps two metadata commits, and advances the local primary ref to the origin tip.

^{Reviewed by Cursor Bugbot for commit ebe73db. Configure here.}

[Copilot]

Pull request overview

This PR fixes a root cause of the “shallow-metadata false-disconnect” issue by changing FetchMetadataTreeOnly to stop using git fetch --depth=1, preventing the CLI from creating shallow boundaries in the user’s repo that later break git merge-base connectivity checks for the metadata branch.

Changes:

• Remove shallow (--depth=1) fetching from FetchMetadataTreeOnly, relying on incremental full-depth fetches and blob filtering when enabled.
• Add a regression test asserting FetchMetadataTreeOnly does not leave the repository in a shallow state and preserves full metadata history.

Reviewed changes

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

File	Description
cmd/entire/cli/git_operations.go	Switch FetchMetadataTreeOnly to full-depth fetch (no --depth=1) to avoid creating shallow boundaries.
cmd/entire/cli/treeless_fetch_full_depth_test.go	Add regression test to ensure the metadata tip-read does not shallow the repo and retains full metadata history.