fix: split Windows manifest cleanup out of the Studio branch

[XucroYuri]

I am working toward a larger Studio contribution, but before sending the frontend itself upstream I wanted to peel off one small fix that kept muddying the branch on Windows.

While regenerating the manifest and running the plugin discovery tests locally, I kept hitting two problems:

• build-manifest could write Windows path separators back into cli-manifest.json, which made the file look changed even when the actual command inventory had not meaningfully changed.
• one of the plugin discovery tests used a symlink setup that is noticeably less reliable on Windows than a directory junction.

So this PR is intentionally small.

It does four things:

• normalize sourceFile paths before writing the manifest
• keep cli-manifest.json newline-stable
• use a directory junction in the Windows plugin discovery test
• add regression coverage around the manifest formatting behavior

I ran:

• npx vitest run src/build-manifest.test.ts src/engine.test.ts src/cli.test.ts src/diagnostic.test.ts --project unit
• npm run typecheck

The bigger thing I am preparing is Studio itself: a frontend workspace for command discovery, readiness checks, execution, and troubleshooting on top of the existing OpenCLI runtime. I left all of that out of this PR on purpose so this patch can stand on its own and be reviewed quickly.