fix: support nested repositories in workspace checkpoints

[4pmtong]

Pull Request

Related Issue

Closes #1901

Description

This fixes workspace checkpoint failures after a task clones an independent Git repository inside a Git-managed Space.

Git reports an untracked nested repository as a single directory entry such as ?? child-repository/. The checkpoint path pipeline normalized the corresponding Path to child-repository, causing path_sources validation to fail after the clone had already completed. The tool outcome was then marked unknown and the Run failed.

The parent Content Repository now treats a verified untracked nested Git root as an independent repository boundary. It excludes that boundary from parent checkpoint/status ownership without modifying ignore files or staging an implicit gitlink. Physical worktree cleanliness remains unchanged so isolated worktrees are not cleaned while they contain an unmerged nested repository.

A regression test covers creating a child repository during a broad terminal mutation and verifies that:

• the parent checkpoint completes without creating a parent commit;
• parent HEAD, state token, and tracked paths remain unchanged;
• the child repository and its committed content remain intact;
• physical worktree safety still detects the nested repository.

Testing Evidence (REQUIRED)

Locally verified command output:

$ uv run --project backend pytest backend/tests/app/workspace_git -q
185 passed in 114.09s

$ uvx ruff check backend/app/workspace_git/backend.py backend/tests/app/workspace_git/test_mutation.py
All checks passed!

$ uvx ruff format --check backend/app/workspace_git/backend.py backend/tests/app/workspace_git/test_mutation.py
2 files already formatted

$ git diff --check
(no output)

• I have included human-verified testing evidence in this PR.
• This PR includes frontend/UI changes, and I attached screenshot(s) or screen recording(s).
• No frontend/UI changes in this PR.

What is the purpose of this pull request?

• Bug fix
• New Feature
• Documentation update
• Other

Contribution Guidelines Acknowledgement

• I have read and agree to the Eigent Contribution Guideline