Fix phantom GeoPackage created from default references config

[harminius]

Problem

Users running the Docker image without overriding references hit a recurring error:

There are pending changes in the local directory - please review and push manually! {'added': [{'path': 'survey.gpkg', ...size: 0...}]}

survey.gpkg doesn't exist in their project - it's a phantom empty file.

Root cause

1. config.yaml.default is baked into the docker image as config.yaml. This example references entry pointing at `survey.gpkg is silently active for everyone.
2. _update_references creates the file if it doesn't exist. The missing survey.gpkg was created as an empty file, then flagged as a pending change and blocked every sync cycle.

Fix

• config.yaml.default: default references to []; keep the example commented for documentation. Reference rewriting is now off unless explicitly configured
• media_sync.py: skip any reference whose file isn't present in the project