[CleanCut]

oxen checkout <branch> deleted any file sitting where the target branch has a directory, unless it was a tracked file with local edits. An untracked file there, or a file put in place of a tracked directory, was lost with no error, while the same untracked file stopped the checkout when the target had a file at that path instead.

Checkout now replaces such a file only when it is the current commit's file at that path, unchanged, and otherwise fails with the "your local changes would be overwritten" error and leaves the working tree as it was. oxen merge --abort still replaces it. This affects local working trees only (the CLI and Python bindings), not oxen-server.

Fixes #1136

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Recent review info

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• Source mode: Auto
• Repository: Oxen-AI/Oxen
• Branch: cleancut/checkout-keep-untracked-file
• File: .coderabbit.yaml
• Commit: 73e2928
• Layers: Repository YAML
• Review profile: ASSERTIVE
• Plan: Essentials
• Run ID: 4f924743-445d-4aed-b022-b6c2a038bfdc

Commits

Reviewing files that changed from the base of the PR and between 0f0f397 and 73e2928.

Files selected for processing: 2

• crates/liboxen/src/core/v_latest/branches.rs
• crates/liboxen/src/repositories/checkout.rs

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📝 Summary

Summary by CodeRabbit

• Bug Fixes
  • Checkout now preserves untracked files and locally modified files when they conflict with a directory in the target branch, and reports an overwrite conflict instead of replacing them.
  • Unmodified tracked files can still be replaced by the target directory, and choosing overwrite restores the directory and its contents.
• Tests
  • Added coverage for file-versus-directory conflicts across branches, including preserved file contents and unchanged checkout state after a conflict.

Checkout now refuses directory replacement when the working-tree file is untracked or fails the unchanged-file checks. Regression tests cover conflict refusal, file preservation, replacement of an unchanged tracked file, and OnConflict::Overwrite.

Changes: Checkout directory replacement conflicts

Layer / File(s)	Summary
Directory replacement conflict handling crates/liboxen/src/core/v_latest/branches.rs, crates/liboxen/src/repositories/checkout.rs	Under OnConflict::Abort, checkout records a conflict if no corresponding from-tree file exists or if the tracked file fails the size and mtime-or-hash checks. Tests verify refusal and content preservation, permitted replacement of an unchanged tracked file, and replacement under OnConflict::Overwrite.

Estimated code review effort: 2 (Simple) | ~12 minutes

Change: Bug fix · Severity of issue fixed: Medium

Possibly related issues

Merge Risk: Minimal · up to 73e29

Checkout appears to preserve conflicting local files while still allowing an unchanged tracked file to be replaced. No actionable merge risk remains after normal checks.

Pre-merge checks: 4

Check name	Status	Explanation
Title check		The title clearly and concisely describes the main checkout change: refusing to delete a file when the target has a directory at that path.
Description check		The description directly explains the checkout behavior, the conditions for replacement, the preserved working tree, and the affected interfaces. It matches the changeset.
Linked Issues check		Issue [#1136] requires checkout to refuse a non-directory entry where the target tree requires a directory, report the local-changes-overwritten error, and preserve the entry. walk_target_tree now p…
Out of Scope Changes check		The changes are limited to checkout conflict handling in crates/liboxen/src/core/v_latest/branches.rs and related checkout regression tests. The OnConflict::Overwrite assertion verifies the docume…

Full details: Linked Issues check

Explanation

Issue [#1136] requires checkout to refuse a non-directory entry where the target tree requires a directory, report the local-changes-overwritten error, and preserve the entry. walk_target_tree now permits replacement under OnConflict::Abort only for an unchanged file from the current tree. Untracked entries and changed tracked entries become conflicts before any replacement. The regression test covers an untracked file, error text, unchanged contents, and unchanged HEAD. The test also covers replacement of an unchanged tracked file and the existing overwrite path.

Full details: Out of Scope Changes check

Explanation

The changes are limited to checkout conflict handling in crates/liboxen/src/core/v_latest/branches.rs and related checkout regression tests. The OnConflict::Overwrite assertion verifies the documented oxen merge --abort behavior. The changes support the linked checkout objective and do not add unrelated product behavior.

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