TS6307 error when building with tsup in monorepo package, but tsc works fine

**Description:**

I'm working in a monorepo setup. In my package, I have the following structure:

```
package
├── src/
│ ├── index.ts
│ └── ref.ts
├── package.json
├── tsconfig.json
```

My `tsconfig.json` includes:

```json
{
"extends": "../../tsconfig.json",
"compilerOptions": {
"composite": true,
"rootDir": "./src",
"moduleResolution": "node",
"outDir": "dist"
},
"include": ["src/**/*"]
}
```

My build script in `package.json` is:

```json
"build": "tsup src/index.ts --clean --format cjs,esm --dts --tsconfig ./tsconfig.json"
```

When I run `npm run build`, I get the following error:

```
error TS6307: File '/package/src/ref.ts' is not listed within the file list of project ''. Projects must list all files or use an 'include' pattern.
```

However, running `npx tsc -p tsconfig.json` works perfectly and generates the expected declaration files.

---

**What I've tried:**

- Changing `moduleResolution` between `node` and `bundler`
- Adjusting the `include` pattern
- Cleaning the `dist` and `.tsbuildinfo` files
- Upgrading `tsup` and `typescript`
- Restarting VS Code

---

**Expected behavior:**

`tsup` should build the package and generate declaration files without TS6307 errors, just like `tsc` does.

---

**Actual behavior:**

`tsup` fails with TS6307, but `tsc` works.

---

**Environment:**

- tsup version: v8.5.0
- typescript version: v5.9.2
- Node.js version: v22.19.0

---

**Additional context:**

Is there a workaround or recommended way to use `tsup` for both JS and declaration file generation in this scenario?

Reproduce the failure with the package's `package.json` build script and `tsconfig.json`, using `src/index.ts` and its `src/ref.ts` import. Compare `tsup src/index.ts --clean --format cjs,esm --dts --tsconfig ./tsconfig.json` with `npx tsc -p tsconfig.json`. Done means the tsup build completes and generates the expected declaration files without TS6307.

Written by the indexing model from the issue text.