Rewrite relative alternates so go-git can follow shared clones

[pjbgf]

https://entire.io/gh/entireio/cli/trails/445

go-git's dotgit.Alternates() strips leading "../" and anchors entries at the filesystem root, so relative objects/info/alternates entries — the shape produced by git clone --shared/--reference — point at non-existent paths. The pre-push checkpoint sync then fails to resolve alternate-resident commits even though git itself reads them.

Wrap both the dotgit and common-git filesystems with an alternates rewriter that resolves relative entries against /objects on read. The rewriter preserves file structure (comments, blanks, absolute entries pass through untouched), caps reads at 4096 bytes, and applies to nested alternate chains via the os-rooted AlternatesFS. Linked worktrees are covered because the wrap applies to the common dir where the alternates file actually lives.

Adds unit tests for the rewriter, integration tests for OpenPath across multiple/nested/linked-worktree relative-alternate layouts, and an e2e test reproducing the shared-clone checkpoint sync failure. Tests that shell out to git get GIT_CONFIG_* isolation so they don't pick up host config.

Support for Windows confirmed via E2E tests:

✓ TestAlternates_RelativeObjectAlternate_CheckpointSync (5.2s)
− TestAttachSessionAddsToExistingCheckpoint
− TestAttachSessionCreatesCheckpoint

---

Note

Medium Risk
Changes how repositories with alternates are opened for all go-git paths (checkpoint sync, tests using OpenPath); behavior is well-tested but incorrect rewriting could break object resolution for shared or worktree layouts.

Overview
go-git can’t resolve relative objects/info/alternates entries (shared/--reference clones). This PR rewrites those paths on read so checkpoint sync and OpenPath can load objects from alternate stores.

On open, dot-git and common-git billy filesystems are wrapped so objects/info/alternates serves in-memory content with relative lines resolved against <git-dir>/objects, matching Git. Comments, blanks, and absolute paths are unchanged; reads are capped at 4KB. The OS-rooted alternates FS applies the same rewrite for nested …/objects/info/alternates files in alternate chains.

Tests: unit coverage for the rewriter; OpenPath integration for single/multiple/nested relative alternates and linked worktrees; e2e pre-push checkpoint sync with a forced relative alternate. IsolateGitConfigEnv and broader GIT_CONFIG_* filtering stabilize tests that call git via os.Environ().

^{Reviewed by Cursor Bugbot for commit 8f14f10. Configure here.}

[Copilot]

Pull request overview

This PR fixes go-git repository opening for shared/reference clones that use relative objects/info/alternates paths, so checkpoint sync can resolve commits stored in alternate object directories.

Changes:

• Adds an alternates rewriter that resolves relative alternates against the owning objects directory.
• Applies the rewriter to dot-git/common-git filesystems and nested alternate chains.
• Adds unit, repository-level, strategy, and e2e coverage for relative alternates and Git config isolation.

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/gitrepo/alternates_rewrite.go	Adds the filesystem wrapper and rewrite helpers for relative alternates.
cmd/entire/cli/gitrepo/alternates_fs.go	Rewrites nested alternate files when go-git follows alternate chains.
cmd/entire/cli/gitrepo/repository.go	Wraps dot-git and common-git filesystems during repository open.
cmd/entire/cli/gitrepo/alternates_rewrite_test.go	Adds unit coverage for alternates rewriting and read limits.
cmd/entire/cli/gitrepo/repository_test.go	Adds OpenPath coverage for single, multiple, nested, and linked-worktree relative alternates.
cmd/entire/cli/testutil/testutil.go	Expands Git config isolation helpers for tests.
cmd/entire/cli/strategy/push_common_test.go	Applies in-process Git config isolation to fetch/rebase tests.
e2e/tests/alternates_test.go	Adds an e2e reproduction for checkpoint sync through a relative alternate.

[cursor]

Cursor Bugbot has reviewed your changes and found 1 potential issue.

^{❌ Bugbot Autofix is OFF. To automatically fix reported issues with cloud agents, enable autofix in the Cursor dashboard.}

Comment @cursor review or bugbot run to trigger another review on this PR

^{Reviewed by Cursor Bugbot for commit 8f14f10. Configure here.}