Feature Request: Better Support for Git Submodules with Independent Biome Configurations

[schickling]

Problem Description

Currently, Biome throws "nested root configuration" errors when a git submodule contains its own biome.json/biome.jsonc file, even when both the parent repository and submodule are independent projects that need their own Biome configurations.

Current Behavior

When working on a parent repository that includes a git submodule, both having their own Biome configurations:

parent-repo/
├── biome.json                    # Parent repo config
├── submodules/
│   └── child-repo/
│       ├── .git                  # Independent git repository
│       └── biome.jsonc           # Child repo config

Biome produces errors like:

Found a nested root configuration, but there's already a root configuration.

Expected Behavior

Biome should gracefully handle git submodules with independent Biome configurations, allowing:

1. Independent Development: Each repository can be developed independently with its own Biome configuration
2. Parent Repository Integration: When working on the parent repository, Biome should either:
   • Automatically detect and respect git submodule boundaries
   • Provide a configuration option to handle submodules appropriately
   • Allow explicit configuration of how to handle submodules

Use Case

This scenario is common in:

• Monorepo with Submodules: A main monorepo includes other monorepos as git submodules
• Vendor Dependencies: Third-party projects included as submodules that have their own tooling
• Shared Libraries: Common libraries developed independently but included in multiple projects
• Microservice Architectures: Where shared components are managed as separate repositories

Real-world example: A my-app monorepo includes the livestore monorepo as a git submodule. Both are independent projects with their own development workflows, CI/CD, and tooling configurations, but need to work together during development.

Current Workarounds and Limitations

Workaround 1: Exclude Submodules

{
  "files": {
    "includes": ["**/*.{js,ts,jsx,tsx}", "!submodules/**"]
  }
}

Limitations:

• Cannot format/lint submodule files from parent repository
• Inconsistent developer experience when working across repository boundaries
• Manual exclusion patterns must be maintained

Workaround 2: Nested Configuration with "root": false

{
  "root": false,
  "extends": "../../biome.json"
}

Limitations:

• Breaks independence of the submodule
• Submodule loses its own configuration preferences
• Creates coupling between independent repositories

Additional Context

• Biome Version: 2.1.0
• Platform: macOS (likely affects all platforms)
• Repository Structure: Monorepo with git submodules
• Development Workflow: Developers work on both parent and submodule simultaneously

This feature would significantly improve Biome's usability in complex repository structures that are common in modern development workflows.

Related Issues

• 🐛 Can't ignore nested biome.json configuration #6509: Can't ignore nested biome.json configuration
• 🐛 Biome is configured to extend a nested config file, it doesn't work as expected #3950: Biome is configured to extend a nested config file, it doesn't work as expected
• 🐛 Nested biome.json files in monorepo not detected #972: Nested biome.json files in monorepo not detected

---

Would appreciate any thoughts from the maintainers on whether this is something that could be supported in future versions of Biome, or if there are alternative approaches we should consider.

🤖 This issue was co-written with Claude

[kneczaj]

The current workaround is including this in biome.json:

  "files": {
    "includes": ["!src/path/to/submodule"]
  }

If the submodule has its own biome, and it is committed with some linting check, then this state makes it linted separately by its own biome config.