Verify latest release

• I verified that the issue exists in the latest pnpm release

pnpm version

No response

Which area(s) of pnpm are affected? (leave empty if unsure)

CLI

Link to the code that reproduces this issue or a replay of the bug

No response

Reproduction steps

In empty directory, start with package.json:

{
  "scripts": {
    "test": "echo Passed!"
  }
}

Running it with pnpm run -r test works:

% pnpm run -r test

> @ test /private/tmp/p
> echo Passed!

Passed!

Now create empty pnpm-workspace.yml, and then pnpm run -r test will break:

% touch pnpm-workspace.yaml
% pnpm run -r test         
No projects matched the filters in "/private/tmp/p"

Describe the Bug

pnpm-workspace.yml without any settings in it impacts pnpm behavior. In particular, it breaks pnpm run -r for non-monorepos.

Expected Behavior

Simply the mere presence of pnpm-workspace.yml doesn't impact run -r. It could only become relevant when there is a packages: section defined. Otherwise, the file might exist for valid reasons, such as being auto-generated when interactively adding onlyBuiltDependencies, bearing non-monorepo overrides, patches, etc.

Which Node.js version are you using?

24.13.0

Which operating systems have you used?

• macOS
• Windows
• Linux

If your OS is a Linux based, which one it is? (Include the version if relevant)

No response