Describe the bug

Sourcebot v4.7.0 seems to have a critical bug that prevents all repository indexing from working. The issue occurs in the repository cloning and configuration process where:

1. Repositories are correctly cloned as bare repositories using git clone --bare
2. Later in the process, the code attempts to read git configuration using GitConfigScope.local (which translates to git config --local)
3. The --local flag is incompatible with bare repositories and fails with: fatal: --local can only be used inside a git repository
4. This causes all repository indexing jobs to fail after 3 retry attempts
5. No repositories can be indexed, making search functionality completely non-functional

Expected Behavior
Repositories should be successfully cloned and indexed, with logs showing:
• Cloned [repository] in X.XXs
• Indexing [repository]...
• Indexed [repository] in X.XXs
• Repo index job for repo [repository] completed

Actual Behavior
Repository indexing fails with the following error pattern:

[backend] | 2025-09-19T10:32:56.025Z error: [repo-manager] Failed to sync repository github.com/sourcebot-dev/sourcebot (id: 1), attempt 1/3. Sleeping for 60s... Error: Error: Failed to set git config /data/.sourcebot/repos/1: fatal: --local can only be used inside a git repository

To reproduce

1. Create a basic config.json file:

{ "$schema": "https://raw.githubusercontent.com/sourcebot-dev/sourcebot/main/schemas/v3/index.json", "connections": { "test-connection": { "type": "github", "repos": [ "sourcebot-dev/sourcebot" ] } } } 

2. Create a docker-compose.yml with Sourcebot v4.7.0:

services: postgres: image: postgres:16 environment: POSTGRES_DB: sourcebot POSTGRES_USER: postgres POSTGRES_PASSWORD: postgres POSTGRES_HOST_AUTH_METHOD: trust volumes: - postgres_data:/var/lib/postgresql/data healthcheck: test: ["CMD-SHELL", "pg_isready -U postgres"] interval: 5s timeout: 5s retries: 5 redis: image: redis:7-alpine volumes: - redis_data:/data healthcheck: test: ["CMD", "redis-cli", "ping"] interval: 5s timeout: 5s retries: 5 sourcebot: image: ghcr.io/sourcebot-dev/sourcebot:latest # v4.7.0 depends_on: postgres: condition: service_healthy redis: condition: service_healthy ports: - "3000:3000" volumes: - .:/data environment: - CONFIG_PATH=/data/config.json - DATABASE_URL=postgresql://postgres:postgres@postgres:5432/sourcebot - REDIS_URL=redis://redis:6379 - DATA_CACHE_DIR=/data/.sourcebot - DATABASE_EMBEDDED=false - SOURCEBOT_LOG_LEVEL=debug volumes: postgres_data: redis_data: 

3. Start the services and monitor the logs.

Sourcebot deployment information

Environment
• Host OS: macOS (also affects Linux deployments)
• Docker: Docker Compose v2+
• Deployment Method: Docker containers with separate PostgreSQL and Redis services

Affected Versions
• Sourcebot: v4.7.0 (latest as of 2025-09-19)
• Status: Critical regression bug

Working Versions
• Sourcebot: v4.6.0 and earlier versions work correctly

Additional information

No response