nx graph and @nx/enforce-module-boundaries break when customizing workspaceLayout.appsDir to src

[denchiklut]

Current Behavior

After customizing the workspace layout in nx.json:

"workspaceLayout": {
    "appsDir": "src",
    "libsDir": "libs"
}

With the following monorepo structure:

- src
  └─ web         // tag: scope:fe
- libs
  └─ uikit       // tag: scope:core
- package.json    // name: "my-org"
- nx.json

Running nx graph shows an unexpected extra project, in addition to the correct ones:
✅ Expected:

• web
• uikit

❌ Actual:

• web
• uikit
• my-org (name from package.json)

This "ghost" root-level project seems to be inferred automatically, which causes issues downstream.

Side Effect
This behavior also breaks the ESLint @nx/enforce-module-boundaries rule:

'@nx/enforce-module-boundaries': [
  'error',
  {
    allow: ['^.*/eslint(\\.base)?\\.config\\.mjs$'],
    depConstraints: [
      {
        sourceTag: 'scope:*',
        onlyDependOnLibsWithTags: ['scope:core'],
      },
    ],
  },
]

Expected Behavior

1. nx graph should only show 2 projects:

• web
• uikit

2. nx lint web should pass.

GitHub Repo

https://github.com/denchiklut/nx-demo

Steps to Reproduce

1. Clone the demo repo: https://github.com/denchiklut/nx-demo
2. Run the project graph: nx graph ➜ You’ll see an unexpected extra project (named after the root package.json).
3. Run lint on the web app: nx lint web ➜ This will fail due to a broken @nx/enforce-module-boundaries rule.
4. Rename the src directory to apps and now both nx graph and nx lint web work as expected.

Nx Report

Node           : 22.13.1
OS             : darwin-arm64
Native Target  : aarch64-macos
yarn           : 1.22.22

nx (global)            : 20.6.4
nx                     : 20.6.4
@nx/js                 : 20.6.4
@nx/jest               : 20.6.4
@nx/eslint             : 20.6.4
@nx/workspace          : 20.6.4
@nx/devkit             : 20.6.4
@nx/eslint-plugin      : 20.6.4
@nx/module-federation  : 20.6.4
@nx/next               : 20.6.4
@nx/node               : 20.6.4
@nx/react              : 20.6.4
@nx/web                : 20.6.4
@nx/webpack            : 20.6.4
typescript             : 5.7.3
---------------------------------------
Registered Plugins:
@nx/js/typescript
@nx/next/plugin
@nx/jest/plugin
@nx/eslint/plugin
---------------------------------------
Cache Usage: 932.00 B / 92.64 GB

Failure Logs

Package Manager Version

No response

Operating System

• macOS
• Linux
• Windows
• Other (Please specify)

Additional Information

No response