feat(01-04): add CLI entry point with setup and info commands

- Create click-based CLI with command group (--config, --verbose options)
- Add 'info' command displaying pipeline version, config hash, data source versions
- Add 'setup' command orchestrating full infrastructure flow:
  - Load config -> create store/provenance
  - Fetch gene universe (with checkpoint-restart)
  - Map Ensembl IDs to HGNC + UniProt
  - Validate mapping quality gates
  - Save to DuckDB with provenance sidecar
- Update pyproject.toml entry point to usher_pipeline.cli.main:cli
- Add .gitignore for data/, *.duckdb, build artifacts, provenance files

src/usher_pipeline/cli/main.py

@@ -0,0 +1,103 @@
+"""Main CLI entry point for usher-pipeline.
+
+Provides command group with global options and subcommands for pipeline operations.
+"""
+
+import logging
+from pathlib import Path
+
+import click
+
+from usher_pipeline import __version__
+from usher_pipeline.config.loader import load_config
+from usher_pipeline.cli.setup_cmd import setup
+
+
+# Configure logging
+logging.basicConfig(
+    level=logging.INFO,
+    format='%(asctime)s - %(name)s - %(levelname)s - %(message)s'
+)
+
+
+@click.group()
+@click.option(
+    '--config',
+    type=click.Path(exists=True, path_type=Path),
+    default='config/default.yaml',
+    help='Path to pipeline configuration YAML file'
+)
+@click.option(
+    '--verbose',
+    is_flag=True,
+    help='Enable verbose logging (DEBUG level)'
+)
+@click.pass_context
+def cli(ctx, config, verbose):
+    """Usher-pipeline: Reproducible pipeline for discovering under-studied cilia/Usher candidate genes.
+
+    Provides data infrastructure, gene ID mapping, evidence layer aggregation,
+    and scoring for candidate gene prioritization.
+    """
+    # Set up context
+    ctx.ensure_object(dict)
+    ctx.obj['config_path'] = config
+    ctx.obj['verbose'] = verbose
+
+    # Set logging level
+    if verbose:
+        logging.getLogger().setLevel(logging.DEBUG)
+        logging.debug("Verbose logging enabled")
+
+
+@cli.command()
+@click.pass_context
+def info(ctx):
+    """Display pipeline information and configuration summary."""
+    config_path = ctx.obj['config_path']
+
+    click.echo(f"Usher Pipeline v{__version__}")
+    click.echo(f"Config: {config_path}")
+    click.echo()
+
+    try:
+        config = load_config(config_path)
+
+        # Display config hash
+        config_hash = config.config_hash()
+        click.echo(f"Config Hash: {config_hash[:16]}...")
+        click.echo()
+
+        # Display data source versions
+        click.echo(click.style("Data Source Versions:", bold=True))
+        click.echo(f"  Ensembl Release: {config.versions.ensembl_release}")
+        click.echo(f"  gnomAD Version:  {config.versions.gnomad_version}")
+        click.echo(f"  GTEx Version:    {config.versions.gtex_version}")
+        click.echo(f"  HPA Version:     {config.versions.hpa_version}")
+        click.echo()
+
+        # Display paths
+        click.echo(click.style("Paths:", bold=True))
+        click.echo(f"  Data Directory: {config.data_dir}")
+        click.echo(f"  Cache Directory: {config.cache_dir}")
+        click.echo(f"  DuckDB Path: {config.duckdb_path}")
+        click.echo()
+
+        # Display API config
+        click.echo(click.style("API Configuration:", bold=True))
+        click.echo(f"  Rate Limit: {config.api.rate_limit_per_second} req/s")
+        click.echo(f"  Max Retries: {config.api.max_retries}")
+        click.echo(f"  Cache TTL: {config.api.cache_ttl_seconds}s")
+        click.echo(f"  Timeout: {config.api.timeout_seconds}s")
+
+    except Exception as e:
+        click.echo(click.style(f"Error loading config: {e}", fg='red'), err=True)
+        ctx.exit(1)
+
+
+# Register setup command
+cli.add_command(setup)
+
+
+if __name__ == '__main__':
+    cli()