Repair stale Codex MCP registrations to current managed arguments

[JordanCoin]

Problem

Codemap now generates managed Codex MCP arguments with an explicit --project-root (and optionally --setup-root). An existing user-level Codex MCP entry still uses the legacy argument shape and configured version 4.3.0, while the installed executable reports dev. codemap doctor correctly reports this as an unrecognized/stale Codemap MCP definition.

This is separate from #156: it does not cause the invalid PostToolUse JSON errors.

Current evidence

• Current source generates managed MCP arguments in cmd/integration_command.go.
• Codex setup rewrites its managed MCP entry in cmd/setup.go.
• Doctor rejects the legacy form in cmd/doctor.go.
• The current user configuration has args = [ "mcp", "--configured-version", "4.3.0", "--integration", "codex-setup" ], which lacks the current root arguments.

TDD acceptance criteria

• Add or extend a failing migration test with a managed legacy Codex MCP definition.
• Setup/plugin repair rewrites that definition to the current executable, configured version, project root, and applicable setup root arguments.
• The repair retains unrelated MCP server definitions byte-for-byte or semantically unchanged.
• codemap doctor recognizes the resulting managed MCP definition.
• Cover both a stale version and legacy no-root argument shape.
• Focused setup/doctor tests and go test ./... pass.

Safety boundary

Do not modify a users global ~/.codex/config.toml during development or tests. Perform a real local integration refresh only after the tested code is merged and with explicit user approval.