feat: add multi-repo workspace support for checkpoints

[amir-prompt]

Summary

• Adds support for workspaces containing multiple independent git repositories as subdirectories
• Previously git-ai failed or only tracked one repository when the workspace root wasn't a git repo
• Now each repository correctly receives its own attribution tracking and git notes

Changes

• find_git_repo_for_path() - detect git repo root from file path
• group_files_by_repository() - group edited files by their containing repo
• filter_agent_run_for_repo() - filter AgentRunResult per repository
• Modified handle_checkpoint() to create checkpoints for each repository
• Added 5 unit tests for the new helper functions

Use Case

workspace/                    (NOT a git repository)
├── project-backend/          (git repo A) → Gets its own checkpoint
├── project-frontend/         (git repo B) → Gets its own checkpoint
└── shared-library/           (git repo C) → Gets its own checkpoint

Test plan

• cargo check passes
• cargo test --lib checkpoint - all 15 tests pass
• cargo test --lib git_ai_handlers::tests - all 5 new tests pass
• Single-repo workflows remain backward compatible

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