write/edit/read submit relative paths so absolute and ~ permission rules never match out-of-worktree files

Description

write, edit, and read pass file paths to the permission layer as path.relative(worktree, filePath). Files outside the worktree are therefore submitted as ../... patterns (e.g. ../.ssh/id_ed25519). Absolute and ~/$HOME-expanded permission rules such as "~/.ssh/**": "deny" never match those relative forms, so a deny rule can be bypassed when a tool edits an out-of-worktree file at a relative path.

Steps to reproduce

1. Configure a permission rule denying an absolute or ~-expanded path, e.g. "~/.ssh/**": "deny".
2. In a session whose worktree is not the home directory, attempt an edit/write/read on a file under that path via a relative /tools path.
3. Observe that the rule does not match the relative submission.

Expected

Rules match regardless of whether the tool passed the path as a relative ../ form, an absolute form, or a ~-expanded form.