Verify passes in a checkout that holds other worktrees #64

Part of the epic "Epic: slice 0, foundations. The repo holds the line, its context is tested, and the platform facts are recorded".

Why. The Maintainer's sessions put git worktrees under .claude/worktrees/ inside the main checkout. tools/check_context.py and tools/check_repo.py walk the whole tree, so in that checkout make verify reports every nested worktree's AGENTS.md, CLAUDE.md and tests as this repo's own: 34 context problems and 14 repo problems on 2026-10-14. Verify passes only in a worktree or a fresh clone. Once the story "Session hooks that check" lands, a session in the main checkout is sent back at every stop.

Done when

• The checks walk only what git tracks, or skip any directory that is another working tree (one holding a .git file). The test is written first and plants a nested worktree.
• clone() in tests/test_tools.py and the copy in tools/mutants.py skip the same directories.
• make verify passes in a checkout that holds .claude/worktrees/.

Needs. Nothing outside the repo. Build it after "Kernel: a Pause stops every act, not only Runs", which edits tools/mutants.py.