Hybrid Git/DVC Tracking in a folder

Questions
1

Hi DVC community,

I’m trying to implement a hybrid tracking approach where DVC manages large binary files (.stl meshes) and Git manages small metadata files (.json) within the same directories. I’m running into a conflict when trying to update DVC tracking after adding new files.

Current Setup

data/
├── models/
│   ├── sample_001_a.stl    # DVC-tracked (large binary ~10-50MB)
│   ├── sample_001_a.json   # Git-tracked (small metadata ~1-2KB)
│   ├── sample_001_b.stl
│   ├── sample_001_b.json
│   └── ...
├── processed/
│   ├── sample_001_x.stl     # DVC-tracked
│   ├── sample_001_x.json    # Git-tracked
│   └── ...
└── raw/
    ├── sample_001.stl       # DVC-tracked
    └── ...

Configuration:

.dvcignore:

data/models/*.json
data/processed/*.json
data/raw/*.json

.gitignore:

/data/raw/*.stl
/data/models/*.stl
/data/processed/*.stl

Existing DVC files:

  • data/models.dvc - tracks the models directory
  • data/processed.dvc - tracks the processed directory
  • data/raw.dvc - tracks the raw directory

Git tracking:

  • All JSON files are tracked by Git (currently 80+ JSON files committed)

The Problem

Initial setup worked fine. But when I add new files (e.g., sample_017_a.stl and sample_017_a.json) and try to update DVC tracking:

$ dvc status
data\models.dvc:
        changed outs:
                modified:           data\models

$ dvc add data/models
ERROR: output 'data\models' is already tracked by SCM (e.g. Git).

The same error occurs with:

  • dvc add data/models --force
  • dvc commit data/models.dvc
  • dvc add data/models/sample_017_a.stl (trying to add individual file)

What I’ve Verified

  1. .dvcignore is configured to exclude JSON files
  2. .gitignore is configured to exclude STL files
  3. git ls-files data/models/ only shows JSON files (not STL files)
  4. DVC status correctly detects the new files

My Questions

  1. Is it possible to use DVC directory tracking with Git tracking some files in the same directory? Even with .dvcignore configured?

  2. How should I update DVC tracking when adding new files to an already-tracked directory that contains Git-tracked files?

  3. Is there a DVC configuration option to allow this hybrid approach?

Why am I keeping the files in the same folder that Git and DVC track?

  • STL files: Large binary meshes (10-50MB each) → Best for DVC cloud storage
  • JSON files: Small text metadata with ground truth labels (1-2KB each) → Best for Git (need diffs, version history, code review)

Separating into different directories would work, but it loses the logical grouping of related files (e.g., sample_001_a.stl and sample_001_a.json belong together).

Environment

  • DVC version: 3.59.2 (pip)

Any guidance would be greatly appreciated! Is this hybrid approach supported, or should I restructure to separate directories?

Thank you!