fix(worktrees): group a bare clone's worktrees under the clone (#1049)

[agegr]

A worktree's project root was the parent of its common git dir. For a bare clone (parent/repo.git) that parent is the folder holding every clone, so the worktrees of all repos there fell into one project group (and parent became an allowed file root), while the clone itself resolved to its own, empty project. "New worktree…" also ran git worktree add from parent, which is not a repository.

Reproduced with real git clone --bare + git worktree add: parent/repo1.git/worktree1 and parent/repo2.git/worktree1 both resolved to parent.

• lib/worktree.ts: repoRootFromCommonDir() — the folder holding the common git dir is the root only when that dir is .git, or a .git file in that folder points at it (the project/.bare layout). Any other bare clone is its own root. Used for project resolution and for getRepoRoot(), so new worktrees are created from the clone (in repo.git-worktrees/).
• inferRemovedWorktree() recognizes a bare clone (HEAD, objects/, refs/) so sessions of a removed worktree still group back under it.
• Normal repos and the .bare layout resolve exactly as before.

Test: real-git regression in lib/worktree.test.mjs (two bare clones under one parent, the .bare layout, adding a worktree, a removed worktree); fails on main. Note in docs/agents/files-and-access.md. tsc, eslint, npm test pass.

Closes #1049

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