D1269 — A Claude Code config or settings file is deleted at {} only if Cartographer created it

Context. D63 kept .claude.json forever ("never deleted"), so an empty-HOME connect→disconnect left a {} behind (#1269). The maintainer decided a file Cartographer created and that is empty after removing our entries is deleted; one that existed before or still holds other keys is kept.

Decision. Replaces D63 point 3. configurator.Apply, registerMCPServer and registerHookSettings record in <baseDir>/.cartographer-created.json (a ledger mapping each Claude Code config/settings file they create, by relative path, to the names of our entries it holds: MCP server names, hook names; written through internal/safewrite). configurator.Remove, removeMCPServer and removeHookEntries delete such a file once it is {} and drop its entry; the provenance also ends when the last of our entries leaves a kept file, or when a register finds the file holding none of them (deleted and recreated by the user). The ledger goes with its last entry. A file absent from the ledger is reduced and kept, even as {}. kiro/opencode stay deletable by content (their files hold only MCP entries, D63). The workspace exclusion list covers the ledger. Dry run decides on the same record.

Discarded alternatives. Content-only deletion ({} means delete): it deletes a user's own pre-existing {} file. A new field in the lockfile or client state: not reachable from internal/configurator. Details: docs/configurator.md §cartographer disconnect.