D63 — Complete prune: empty directories with boundaries, MCP configs reduced to empty (WP7)

Context. A connect→disconnect round trip did not return the filesystem to its initial state: PruneManaged ran os.Remove on the individual ManagedFile entries but never on the containing directories left empty; configurator.Remove left {"mcpServers": {}} on disk once the only entry was removed.

Decision. 1. Empty directories (pruneEmptyDirs). After removing a managed file, it walks up the parent directories deleting them if empty, always stopping at a known root (.claude, .codex, .kiro, .opencode, .config, .config/opencode, or BaseDir). os.Remove (never os.RemoveAll) fails on its own on a non-empty directory, so a user file/other artifact stops the ascent without an explicit check. 2. MCP configs reduced to empty. If the server map ends up empty, the key is deleted; for files dedicated solely to MCP config (kiro, opencode) the whole file is deleted if nothing else remains. 3. Absolute invariant: .claude.json is never deleted (shared state broader than Claude Code) — it stays reduced to {}, a residue accepted by construction. 4. End-to-end test (TestRoundTrip_ConnectDisconnect_NessunResiduo) verifies, with a filepath.Walk before/after, that the only difference is the set of exceptions above and that pre-existing user files survive. Discarded alternatives. os.RemoveAll on the providers' directories (it would delete content not managed by Cartographer); always deleting the MCP config file when the entry is removed (wrong for .claude.json, broader shared state). Details: docs/configurator.md §cartographer disconnect.