pnpm deploy generate multiple deploy target directories in different directories

[await-ovo]

pnpm version: 8.6.10

Code to reproduce the issue:

As commented in #6697 (comment), give a workspaces with the following directory structure:

./
├── project-1
│   └── package.json
├── project-3
│   └── package.json
├── sub-dir
│   └── project-2
│       └── package.json
├── package.json
└── pnpm-workspace.yaml


// project-1/package.json
{
	"name": "project-1",
	"version": "1.0.0",
	"dependencies": {
		"is-positive": "1.0.0"
	}
}

// project-3/package.json
{
	"name": "project-3",
	"version": "2.0.0",
	"dependencies": {
		"is-number": "1.0.0"
	}
}

// sub-dir/project-2/package.json
{
	"name": "project-2",
	"version": "2.0.0",
	"dependencies": {
		"is-odd": "1.0.0"
	}
}

// pnpm-workspace.yaml
packages:
  - project-1
  - project-3
  - sub-dir/project-2

After run pnpm --filter project-1 deploy ./dist, you will find that dist directory occurs in the project root directory and ./sub-dir.

Expected behavior:

Deploy target directory(./dist) should only generated to project root directory.

Actual behavior:

Deploy generate multiple deploy target directories in different directories

Additional information:

• node -v prints: v16.15.1
• Windows, macOS, or Linux?: macOS

[await-ovo]

In addition, when dedupe-peer-dependents=true, I wonder if it is possible to filter out unselected packages in linkPackages, so that there should be no dependencies of other packages in node_modules of the deploy target. I'm not sure if this approach is doable or if there are any additional issues? What's your opinion on this? cc @zkochan Thanks ~