Mitosis does not always accurately delete old files

Ran into a tricky bug the other day. Had a file `src/helpers/foo.ts`, and moved it to `src/helpers/foo/index.ts` to be able to add helpers. Unfortunately, the `clean()` function will only delete outputs that match the _current_ list of existing files. Since there was no longer a `src/helpers/foo.ts`, `clean()` did not attempt to delete it.

We don't want to blindly delete the entire output dir. We have cases where we have files there that need to stay, such as a `dist/package.json`, etc.

https://github.com/BuilderIO/mitosis/blob/main/packages/cli/src/build/build.ts#L94-L102

Start in packages/cli/src/build/build.ts around lines 94-102 and trace how clean() determines which outputs to delete. Reproduce the file move from src/helpers/foo.ts to src/helpers/foo/index.ts, while checking that files such as dist/package.json remain untouched. Done means obsolete outputs are removed without deleting unrelated files in the output directory.

Written by the indexing model from the issue text.