Error: Source file not found

### Reproduction link or steps

1. Clone https://github.com/issueset/tsdown-composite-build-issue and install 
2. If I run tsdown directly, I will get the following error:

```bash
$ rm -rf dist; pnpm run build:tsdown

> tsdown-composite@1.0.0 build:tsdown /private/tmp/tsdown-composite
> tsdown

ℹ tsdown v0.12.5 powered by rolldown v1.0.0-beta.10-commit.87188ed
ℹ Using tsdown config: /private/tmp/tsdown-composite/tsdown.config.ts
ℹ entry: src/dom/dom.ts, src/node/node.ts
ℹ tsconfig: tsconfig.json
ℹ Build start

  ERROR  Error: Build failed with 2 errors:

[plugin rolldown-plugin-dts:generate]
Error: Source file not found: /private/tmp/tsdown-composite/src/dom/dom.ts
    at createTsProgram (file:///private/tmp/tsdown-composite/node_modules/.pnpm/rolldown-plugin-dts@0.13.6_rolldown@1.0.0-beta.10-commit.87188ed_typescript@5.8.3/node_modules/rolldown-plugin-dts/dist/tsc-yr4fe8f_.js:93:25)
    at createOrGetTsModule (file:///private/tmp/tsdown-composite/node_modules/.pnpm/rolldown-plugin-dts@0.13.6_rolldown@1.0.0-beta.10-commit.87188ed_typescript@5.8.3/node_modules/rolldown-plugin-dts/dist/tsc-yr4fe8f_.js:72:17)
    at tscEmit (file:///private/tmp/tsdown-composite/node_modules/.pnpm/rolldown-plugin-dts@0.13.6_rolldown@1.0.0-beta.10-commit.87188ed_typescript@5.8.3/node_modules/rolldown-plugin-dts/dist/tsc-yr4fe8f_.js:100:17)
    at PluginContextImpl.handler (file:///private/tmp/tsdown-composite/node_modules/.pnpm/rolldown-plugin-dts@0.13.6_rolldown@1.0.0-beta.10-commit.87188ed_typescript@5.8.3/node_modules/rolldown-plugin-dts/dist/index.js:744:20)
    at plugin (file:///private/tmp/tsdown-composite/node_modules/.pnpm/rolldown@1.0.0-beta.10-commit.87188ed/node_modules/rolldown/dist/shared/src-euELSICh.mjs:2748:30)
    at plugin.<computed> (file:///private/tmp/tsdown-composite/node_modules/.pnpm/rolldown@1.0.0-beta.10-commit.87188ed/node_modules/rolldown/dist/shared/src-euELSICh.mjs:3538:18)
[plugin rolldown-plugin-dts:generate]
Error: Source file not found: /private/tmp/tsdown-composite/src/node/node.ts
    at createTsProgram (file:///private/tmp/tsdown-composite/node_modules/.pnpm/rolldown-plugin-dts@0.13.6_rolldown@1.0.0-beta.10-commit.87188ed_typescript@5.8.3/node_modules/rolldown-plugin-dts/dist/tsc-yr4fe8f_.js:93:25)
    at createOrGetTsModule (file:///private/tmp/tsdown-composite/node_modules/.pnpm/rolldown-plugin-dts@0.13.6_rolldown@1.0.0-beta.10-commit.87188ed_typescript@5.8.3/node_modules/rolldown-plugin-dts/dist/tsc-yr4fe8f_.js:72:17)
    at tscEmit (file:///private/tmp/tsdown-composite/node_modules/.pnpm/rolldown-plugin-dts@0.13.6_rolldown@1.0.0-beta.10-commit.87188ed_typescript@5.8.3/node_modules/rolldown-plugin-dts/dist/tsc-yr4fe8f_.js:100:17)
    at PluginContextImpl.handler (file:///private/tmp/tsdown-composite/node_modules/.pnpm/rolldown-plugin-dts@0.13.6_rolldown@1.0.0-beta.10-commit.87188ed_typescript@5.8.3/node_modules/rolldown-plugin-dts/dist/index.js:744:20)
    at plugin (file:///private/tmp/tsdown-composite/node_modules/.pnpm/rolldown@1.0.0-beta.10-commit.87188ed/node_modules/rolldown/dist/shared/src-euELSICh.mjs:2748:30)
    at plugin.<computed> (file:///private/tmp/tsdown-composite/node_modules/.pnpm/rolldown@1.0.0-beta.10-commit.87188ed/node_modules/rolldown/dist/shared/src-euELSICh.mjs:3538:18)
    at normalizeErrors (file:///private/tmp/tsdown-composite/node_modules/.pnpm/rolldown@1.0.0-beta.10-commit.87188ed/node_modules/rolldown/dist/shared/src-euELSICh.mjs:2218:18)
    at handleOutputErrors (file:///private/tmp/tsdown-composite/node_modules/.pnpm/rolldown@1.0.0-beta.10-commit.87188ed/node_modules/rolldown/dist/shared/src-euELSICh.mjs:3148:34)
    at transformToRollupOutput (file:///private/tmp/tsdown-composite/node_modules/.pnpm/rolldown@1.0.0-beta.10-commit.87188ed/node_modules/rolldown/dist/shared/src-euELSICh.mjs:3142:2)
    at RolldownBuild.write (file:///private/tmp/tsdown-composite/node_modules/.pnpm/rolldown@1.0.0-beta.10-commit.87188ed/node_modules/rolldown/dist/shared/src-euELSICh.mjs:4292:10)
    at async build (file:///private/tmp/tsdown-composite/node_modules/.pnpm/rolldown@1.0.0-beta.10-commit.87188ed/node_modules/rolldown/dist/shared/src-euELSICh.mjs:4330:22)
    at async file:///private/tmp/tsdown-composite/node_modules/.pnpm/tsdown@0.12.5_typescript@5.8.3/node_modules/tsdown/dist/index.js:837:24
    at async Promise.all (index 0)
    at async rebuild (file:///private/tmp/tsdown-composite/node_modules/.pnpm/tsdown@0.12.5_typescript@5.8.3/node_modules/tsdown/dist/index.js:830:3)
    at async buildSingle (file:///private/tmp/tsdown-composite/node_modules/.pnpm/tsdown@0.12.5_typescript@5.8.3/node_modules/tsdown/dist/index.js:820:2)
    at async Promise.all (index 0)
    at async build (file:///private/tmp/tsdown-composite/node_modules/.pnpm/tsdown@0.12.5_typescript@5.8.3/node_modules/tsdown/dist/index.js:792:19)
    at async CAC.<anonymous> (file:///private/tmp/tsdown-composite/node_modules/.pnpm/tsdown@0.12.5_typescript@5.8.3/node_modules/tsdown/dist/run.js:22:2)
    at async runCLI (file:///private/tmp/tsdown-composite/node_modules/.pnpm/tsdown@0.12.5_typescript@5.8.3/node_modules/tsdown/dist/run.js:40:3) {
  errors: [Getter/Setter]
}

 ELIFECYCLE  Command failed with exit code 1.
```

3. If I run `tsc --build` firstly, then running `tsdown` is fine:

```bash
$ rm -rf dist; pnpm run build:tsc; pnpm run build:tsdown

> tsdown-composite@1.0.0 build:tsc /private/tmp/tsdown-composite
> tsc --build .


> tsdown-composite@1.0.0 build:tsdown /private/tmp/tsdown-composite
> tsdown

ℹ tsdown v0.12.5 powered by rolldown v1.0.0-beta.10-commit.87188ed
ℹ Using tsdown config: /private/tmp/tsdown-composite/tsdown.config.ts
ℹ entry: src/dom/dom.ts, src/node/node.ts
ℹ tsconfig: tsconfig.json
ℹ Build start
ℹ dist/dist_tsdown/node/node.js    0.17 kB │ gzip: 0.15 kB
ℹ dist/dist_tsdown/dom/dom.js      0.16 kB │ gzip: 0.15 kB
ℹ dist/dist_tsdown/dom/dom.d.ts    0.01 kB │ gzip: 0.03 kB
ℹ dist/dist_tsdown/node/node.d.ts  0.01 kB │ gzip: 0.03 kB
ℹ 4 files, total: 0.35 kB
✔ Build complete in 323ms
```

### What is expected?

No error.

### What is actually happening?

Error shown as above. 

### Any additional comments?

The repo above has 3 different tsconfig files:


- `tsconfig.dom.json`: Only includes .ts files under `src/dom/`. It ensures that all files under `src/dom/` don't use Node.js types.
- `tsconfig.node.json`: Only includes .ts files under `src/node/`. It ensures that all files under `src/node/` don't use browser types.
- `tsconfig.json`: A root tsconfig.json that uses `references` to includes other two tsconfig files. 


This a good pattern for a large TypeScript project. It improves both type checking soundness and also the performance (e.g., `tsc` doesn't need to re-compile `src/dom/` if only `src/node/` get changed`)


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Error: Source file not found #286

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Error: Source file not found #286

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