Reproduction link or steps

https://github.com/alpheusmtx/tsdown-unbundle-src-wrapped

What is expected?

what is expected:

./src/index.ts -> ./dist/index.js
./src/sub.ts -> ./dist/sub.js

What is actually happening?

what is actually happening:

./src/index.ts -> ./dist/index.js
./src/sub.ts -> ./dist/src/sub.js

Any additional comments?

The situation only happened when the entry option being declared as an object instead of string:

// ok

import { defineConfig } from "tsdown";

export default defineConfig({
    entry: "./src/index.ts",
});

// not ok

import { defineConfig } from "tsdown";

export default defineConfig({
    entry: {
        index: "./src/index.ts",
    },
});