Add support for worktrees

Problem

Shortcake should work correctly when invoked from a Git linked worktree, not only from the primary checkout.

Current status

Some low-level paths now use pygit2 repository discovery and repo.path, but worktree support is not covered end-to-end. There are still Git-local state files and recovery paths that need explicit verification in linked worktrees.

Remaining work

• Add tests that run core commands from a linked worktree.
• Verify Git-local state files are stored in the correct git dir for that worktree.
• Audit state/cache paths such as PR cache, restack state, and future transaction/recovery files.
• Verify branch switching, restack/continue/abort, submit, pull, sync, and UI startup from a worktree.

Acceptance criteria

• Commands behave the same from the main worktree and a linked worktree.
• No command assumes .git is a directory in the working tree.
• State cleanup and recovery work from linked worktrees.

Begin with the existing pygit2 repository-discovery and repo.path handling, then exercise branch switching, restack/continue/abort, submit, pull, sync, and UI startup from a linked worktree. Audit the PR cache, restack state, and other Git-local state or recovery paths; done means core commands behave like they do in the main worktree and cleanup and recovery work correctly.