Changes required for matomo-scoper:
- add include-namespaces config options to allowlist namespaces to prefix
- add --in-place cmdline option to allow replacing files in place
- add --force-no-global-alias option to allow disabling the behavior that aliases global classes that were not prefixed
- do not convert internal function names to fully qualified if original code does not do this already (required to get some matomo tests to pass)