Implement database storage layer

- Add connection pool configuration (pool_size, max_overflow, timeout, recycle)
- Add transaction management utilities (transaction, savepoint, retry_on_deadlock)
- Create repository pattern classes for all entities (Project, Package, Artifact, Tag, Upload)
- Implement ref_count decrement and cleanup service
- Add query helper functions (search, filtering, pagination, stats)
- Add database constraints (check_ref_count_non_negative, check_size_positive)
- Add performance indexes (idx_artifacts_ref_count, composite indexes for packages/tags)
- Initialize Alembic migrations for future schema changes

backend/alembic.ini

@@ -0,0 +1,83 @@
+# Alembic Configuration File
+
+[alembic]
+# path to migration scripts
+script_location = alembic
+
+# template used to generate migration files
+# file_template = %%(rev)s_%%(slug)s
+
+# sys.path path, will be prepended to sys.path if present.
+prepend_sys_path = .
+
+# timezone to use when rendering the date within the migration file
+# as well as the filename.
+# If specified, requires the python-dateutil library
+# timezone =
+
+# max length of characters to apply to the "slug" field
+# truncate_slug_length = 40
+
+# set to 'true' to run the environment during the 'revision' command,
+# regardless of autogenerate
+# revision_environment = false
+
+# set to 'true' to allow .pyc and .pyo files without a source .py file
+# to be detected as revisions in the versions/ directory
+# sourceless = false
+
+# version location specification
+# version_locations = %(here)s/bar:%(here)s/bat:alembic/versions
+
+# version path separator
+# version_path_separator = :
+
+# set to 'true' to search source files recursively
+# in each "version_locations" directory
+# recursive_version_locations = false
+
+# the output encoding used when revision files are written from script.py.mako
+# output_encoding = utf-8
+
+# Database URL - will be overridden by env.py
+sqlalchemy.url = driver://user:pass@localhost/dbname
+
+
+[post_write_hooks]
+# post_write_hooks defines scripts or Python functions that are run
+# on newly generated revision scripts.
+
+# Logging configuration
+[loggers]
+keys = root,sqlalchemy,alembic
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARN
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S

backend/alembic/README

@@ -0,0 +1,27 @@
+Alembic Migrations for Orchard
+
+This directory contains database migration scripts managed by Alembic.
+
+Common Commands:
+  # Generate a new migration (autogenerate from model changes)
+  alembic revision --autogenerate -m "description of changes"
+
+  # Apply all pending migrations
+  alembic upgrade head
+
+  # Rollback one migration
+  alembic downgrade -1
+
+  # Show current migration status
+  alembic current
+
+  # Show migration history
+  alembic history
+
+  # Generate SQL without applying (for review)
+  alembic upgrade head --sql
+
+Notes:
+- Always review autogenerated migrations before applying
+- Test migrations in development before applying to production
+- Migrations are stored in the versions/ directory

backend/alembic/env.py

@@ -0,0 +1,95 @@
+"""
+Alembic migration environment configuration.
+"""
+
+from logging.config import fileConfig
+import sys
+from pathlib import Path
+
+from sqlalchemy import engine_from_config
+from sqlalchemy import pool
+
+from alembic import context
+
+# Add the app directory to path for imports
+sys.path.insert(0, str(Path(__file__).parent.parent))
+
+from app.config import get_settings
+from app.models import Base
+
+# this is the Alembic Config object, which provides
+# access to the values within the .ini file in use.
+config = context.config
+
+# Get database URL from settings
+settings = get_settings()
+config.set_main_option("sqlalchemy.url", settings.database_url)
+
+# Interpret the config file for Python logging.
+# This line sets up loggers basically.
+if config.config_file_name is not None:
+    fileConfig(config.config_file_name)
+
+# add your model's MetaData object here
+# for 'autogenerate' support
+target_metadata = Base.metadata
+
+# other values from the config, defined by the needs of env.py,
+# can be acquired:
+# my_important_option = config.get_main_option("my_important_option")
+# ... etc.
+
+
+def run_migrations_offline() -> None:
+    """Run migrations in 'offline' mode.
+
+    This configures the context with just a URL
+    and not an Engine, though an Engine is acceptable
+    here as well.  By skipping the Engine creation
+    we don't even need a DBAPI to be available.
+
+    Calls to context.execute() here emit the given string to the
+    script output.
+
+    """
+    url = config.get_main_option("sqlalchemy.url")
+    context.configure(
+        url=url,
+        target_metadata=target_metadata,
+        literal_binds=True,
+        dialect_opts={"paramstyle": "named"},
+    )
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def run_migrations_online() -> None:
+    """Run migrations in 'online' mode.
+
+    In this scenario we need to create an Engine
+    and associate a connection with the context.
+
+    """
+    connectable = engine_from_config(
+        config.get_section(config.config_ini_section, {}),
+        prefix="sqlalchemy.",
+        poolclass=pool.NullPool,
+    )
+
+    with connectable.connect() as connection:
+        context.configure(
+            connection=connection,
+            target_metadata=target_metadata,
+            compare_type=True,  # Detect column type changes
+            compare_server_default=True,  # Detect default value changes
+        )
+
+        with context.begin_transaction():
+            context.run_migrations()
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()

backend/alembic/script.py.mako

@@ -0,0 +1,26 @@
+"""${message}
+
+Revision ID: ${up_revision}
+Revises: ${down_revision | comma,n}
+Create Date: ${create_date}
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+${imports if imports else ""}
+
+# revision identifiers, used by Alembic.
+revision: str = ${repr(up_revision)}
+down_revision: Union[str, None] = ${repr(down_revision)}
+branch_labels: Union[str, Sequence[str], None] = ${repr(branch_labels)}
+depends_on: Union[str, Sequence[str], None] = ${repr(depends_on)}
+
+
+def upgrade() -> None:
+    ${upgrades if upgrades else "pass"}
+
+
+def downgrade() -> None:
+    ${downgrades if downgrades else "pass"}

backend/app/config.py

@@ -18,6 +18,12 @@ class Settings(BaseSettings):
     database_dbname: str = "orchard"
     database_sslmode: str = "disable"
 
+    # Database connection pool settings
+    database_pool_size: int = 5  # Number of connections to keep open
+    database_max_overflow: int = 10  # Max additional connections beyond pool_size
+    database_pool_timeout: int = 30  # Seconds to wait for a connection from pool
+    database_pool_recycle: int = 1800  # Recycle connections after this many seconds (30 min)
+
     # S3
     s3_endpoint: str = ""
     s3_region: str = "us-east-1"

backend/app/database.py

@@ -1,7 +1,10 @@
-from sqlalchemy import create_engine, text
+from sqlalchemy import create_engine, text, event
 from sqlalchemy.orm import sessionmaker, Session
+from sqlalchemy.pool import QueuePool
 from typing import Generator
+from contextlib import contextmanager
 import logging
+import time
 
 from .config import get_settings
 from .models import Base
@@ -9,10 +12,44 @@ from .models import Base
 settings = get_settings()
 logger = logging.getLogger(__name__)
 
-engine = create_engine(settings.database_url, pool_pre_ping=True)
+# Create engine with connection pool configuration
+engine = create_engine(
+    settings.database_url,
+    pool_pre_ping=True,  # Check connection health before using
+    poolclass=QueuePool,
+    pool_size=settings.database_pool_size,
+    max_overflow=settings.database_max_overflow,
+    pool_timeout=settings.database_pool_timeout,
+    pool_recycle=settings.database_pool_recycle,
+)
+
 SessionLocal = sessionmaker(autocommit=False, autoflush=False, bind=engine)
 
 
+# Connection pool monitoring
+@event.listens_for(engine, "checkout")
+def receive_checkout(dbapi_connection, connection_record, connection_proxy):
+    """Log when a connection is checked out from the pool"""
+    logger.debug(f"Connection checked out from pool: {id(dbapi_connection)}")
+
+
+@event.listens_for(engine, "checkin")
+def receive_checkin(dbapi_connection, connection_record):
+    """Log when a connection is returned to the pool"""
+    logger.debug(f"Connection returned to pool: {id(dbapi_connection)}")
+
+
+def get_pool_status() -> dict:
+    """Get current connection pool status for monitoring"""
+    pool = engine.pool
+    return {
+        "pool_size": pool.size(),
+        "checked_out": pool.checkedout(),
+        "overflow": pool.overflow(),
+        "checked_in": pool.checkedin(),
+    }
+
+
 def init_db():
     """Create all tables and run migrations"""
     Base.metadata.create_all(bind=engine)
@@ -62,6 +99,51 @@ def _run_migrations():
             END IF;
         END $$;
         """,
+        # Add ref_count index and constraints for artifacts
+        """
+        DO $$
+        BEGIN
+            -- Add ref_count index
+            IF NOT EXISTS (
+                SELECT 1 FROM pg_indexes WHERE indexname = 'idx_artifacts_ref_count'
+            ) THEN
+                CREATE INDEX idx_artifacts_ref_count ON artifacts(ref_count);
+            END IF;
+
+            -- Add ref_count >= 0 constraint
+            IF NOT EXISTS (
+                SELECT 1 FROM pg_constraint WHERE conname = 'check_ref_count_non_negative'
+            ) THEN
+                ALTER TABLE artifacts ADD CONSTRAINT check_ref_count_non_negative CHECK (ref_count >= 0);
+            END IF;
+        END $$;
+        """,
+        # Add composite indexes for packages and tags
+        """
+        DO $$
+        BEGIN
+            -- Composite index for package lookup by project and name
+            IF NOT EXISTS (
+                SELECT 1 FROM pg_indexes WHERE indexname = 'idx_packages_project_name'
+            ) THEN
+                CREATE UNIQUE INDEX idx_packages_project_name ON packages(project_id, name);
+            END IF;
+
+            -- Composite index for tag lookup by package and name
+            IF NOT EXISTS (
+                SELECT 1 FROM pg_indexes WHERE indexname = 'idx_tags_package_name'
+            ) THEN
+                CREATE UNIQUE INDEX idx_tags_package_name ON tags(package_id, name);
+            END IF;
+
+            -- Composite index for recent tags queries
+            IF NOT EXISTS (
+                SELECT 1 FROM pg_indexes WHERE indexname = 'idx_tags_package_created_at'
+            ) THEN
+                CREATE INDEX idx_tags_package_created_at ON tags(package_id, created_at);
+            END IF;
+        END $$;
+        """,
     ]
 
     with engine.connect() as conn:
@@ -80,3 +162,75 @@ def get_db() -> Generator[Session, None, None]:
         yield db
     finally:
         db.close()
+
+
+@contextmanager
+def transaction(db: Session):
+    """
+    Context manager for explicit transaction management with savepoint support.
+
+    Usage:
+        with transaction(db):
+            # operations here
+            # automatically commits on success, rolls back on exception
+    """
+    try:
+        yield db
+        db.commit()
+    except Exception:
+        db.rollback()
+        raise
+
+
+@contextmanager
+def savepoint(db: Session, name: str = None):
+    """
+    Create a savepoint for partial rollback support.
+
+    Usage:
+        with savepoint(db, "my_savepoint"):
+            # operations here
+            # rolls back to savepoint on exception, but doesn't rollback whole transaction
+    """
+    savepoint_obj = db.begin_nested()
+    try:
+        yield savepoint_obj
+        savepoint_obj.commit()
+    except Exception:
+        savepoint_obj.rollback()
+        raise
+
+
+def retry_on_deadlock(func, max_retries: int = 3, delay: float = 0.1):
+    """
+    Decorator/wrapper to retry operations on deadlock detection.
+
+    Usage:
+        @retry_on_deadlock
+        def my_operation(db):
+            ...
+
+    Or:
+        retry_on_deadlock(lambda: my_operation(db))()
+    """
+    import functools
+    from sqlalchemy.exc import OperationalError
+
+    @functools.wraps(func)
+    def wrapper(*args, **kwargs):
+        last_exception = None
+        for attempt in range(max_retries):
+            try:
+                return func(*args, **kwargs)
+            except OperationalError as e:
+                # Check for deadlock error codes (PostgreSQL: 40P01, MySQL: 1213)
+                error_str = str(e).lower()
+                if "deadlock" in error_str or "40p01" in error_str:
+                    last_exception = e
+                    logger.warning(f"Deadlock detected, retrying (attempt {attempt + 1}/{max_retries})")
+                    time.sleep(delay * (attempt + 1))  # Exponential backoff
+                else:
+                    raise
+        raise last_exception
+
+    return wrapper

backend/app/models.py

@@ -53,6 +53,7 @@ class Package(Base):
         Index("idx_packages_name", "name"),
         Index("idx_packages_format", "format"),
         Index("idx_packages_platform", "platform"),
+        Index("idx_packages_project_name", "project_id", "name", unique=True),  # Composite unique index
         CheckConstraint(
             "format IN ('generic', 'npm', 'pypi', 'docker', 'deb', 'rpm', 'maven', 'nuget', 'helm')",
             name="check_package_format"
@@ -84,6 +85,9 @@ class Artifact(Base):
     __table_args__ = (
         Index("idx_artifacts_created_at", "created_at"),
         Index("idx_artifacts_created_by", "created_by"),
+        Index("idx_artifacts_ref_count", "ref_count"),  # For cleanup queries
+        CheckConstraint("ref_count >= 0", name="check_ref_count_non_negative"),
+        CheckConstraint("size > 0", name="check_size_positive"),
     )
 
 
@@ -104,6 +108,8 @@ class Tag(Base):
     __table_args__ = (
         Index("idx_tags_package_id", "package_id"),
         Index("idx_tags_artifact_id", "artifact_id"),
+        Index("idx_tags_package_name", "package_id", "name", unique=True),  # Composite unique index
+        Index("idx_tags_package_created_at", "package_id", "created_at"),  # For recent tags queries
     )
 
 

backend/app/repositories/__init__.py

@@ -0,0 +1,22 @@
+"""
+Repository pattern implementation for data access layer.
+
+Repositories abstract database operations from business logic,
+providing clean interfaces for CRUD operations on each entity.
+"""
+
+from .base import BaseRepository
+from .project import ProjectRepository
+from .package import PackageRepository
+from .artifact import ArtifactRepository
+from .tag import TagRepository
+from .upload import UploadRepository
+
+__all__ = [
+    "BaseRepository",
+    "ProjectRepository",
+    "PackageRepository",
+    "ArtifactRepository",
+    "TagRepository",
+    "UploadRepository",
+]

backend/app/repositories/artifact.py

@@ -0,0 +1,157 @@
+"""
+Artifact repository for data access operations.
+"""
+
+from typing import Optional, List, Tuple
+from sqlalchemy.orm import Session
+from sqlalchemy import func, or_
+from uuid import UUID
+
+from .base import BaseRepository
+from ..models import Artifact, Tag, Upload, Package, Project
+
+
+class ArtifactRepository(BaseRepository[Artifact]):
+    """Repository for Artifact entity operations."""
+
+    model = Artifact
+
+    def get_by_sha256(self, sha256: str) -> Optional[Artifact]:
+        """Get artifact by SHA256 hash (primary key)."""
+        return self.db.query(Artifact).filter(Artifact.id == sha256).first()
+
+    def exists_by_sha256(self, sha256: str) -> bool:
+        """Check if artifact with SHA256 exists."""
+        return self.db.query(
+            self.db.query(Artifact).filter(Artifact.id == sha256).exists()
+        ).scalar()
+
+    def create_artifact(
+        self,
+        sha256: str,
+        size: int,
+        s3_key: str,
+        created_by: str,
+        content_type: Optional[str] = None,
+        original_name: Optional[str] = None,
+        format_metadata: Optional[dict] = None,
+    ) -> Artifact:
+        """Create a new artifact."""
+        artifact = Artifact(
+            id=sha256,
+            size=size,
+            s3_key=s3_key,
+            created_by=created_by,
+            content_type=content_type,
+            original_name=original_name,
+            format_metadata=format_metadata or {},
+            ref_count=1,
+        )
+        self.db.add(artifact)
+        self.db.flush()
+        return artifact
+
+    def increment_ref_count(self, artifact: Artifact) -> Artifact:
+        """Increment artifact reference count."""
+        artifact.ref_count += 1
+        self.db.flush()
+        return artifact
+
+    def decrement_ref_count(self, artifact: Artifact) -> Artifact:
+        """
+        Decrement artifact reference count.
+        Returns the artifact with updated count.
+        Does not delete the artifact even if ref_count reaches 0.
+        """
+        if artifact.ref_count > 0:
+            artifact.ref_count -= 1
+            self.db.flush()
+        return artifact
+
+    def get_orphaned_artifacts(self, limit: int = 100) -> List[Artifact]:
+        """Get artifacts with ref_count = 0 (candidates for cleanup)."""
+        return (
+            self.db.query(Artifact)
+            .filter(Artifact.ref_count == 0)
+            .limit(limit)
+            .all()
+        )
+
+    def get_artifacts_without_tags(self, limit: int = 100) -> List[Artifact]:
+        """Get artifacts that have no tags pointing to them."""
+        # Subquery to find artifact IDs that have tags
+        tagged_artifacts = self.db.query(Tag.artifact_id).distinct().subquery()
+
+        return (
+            self.db.query(Artifact)
+            .filter(~Artifact.id.in_(tagged_artifacts))
+            .limit(limit)
+            .all()
+        )
+
+    def find_by_package(
+        self,
+        package_id: UUID,
+        page: int = 1,
+        limit: int = 20,
+        content_type: Optional[str] = None,
+    ) -> Tuple[List[Artifact], int]:
+        """Find artifacts uploaded to a package."""
+        # Get distinct artifact IDs from uploads
+        artifact_ids_subquery = (
+            self.db.query(func.distinct(Upload.artifact_id))
+            .filter(Upload.package_id == package_id)
+            .subquery()
+        )
+
+        query = self.db.query(Artifact).filter(Artifact.id.in_(artifact_ids_subquery))
+
+        if content_type:
+            query = query.filter(Artifact.content_type == content_type)
+
+        total = query.count()
+        offset = (page - 1) * limit
+        artifacts = query.order_by(Artifact.created_at.desc()).offset(offset).limit(limit).all()
+
+        return artifacts, total
+
+    def get_referencing_tags(self, artifact_id: str) -> List[Tuple[Tag, Package, Project]]:
+        """Get all tags referencing this artifact with package and project info."""
+        return (
+            self.db.query(Tag, Package, Project)
+            .join(Package, Tag.package_id == Package.id)
+            .join(Project, Package.project_id == Project.id)
+            .filter(Tag.artifact_id == artifact_id)
+            .all()
+        )
+
+    def search(self, query_str: str, limit: int = 10) -> List[Tuple[Tag, Artifact, str, str]]:
+        """
+        Search artifacts by tag name or original filename.
+        Returns (tag, artifact, package_name, project_name) tuples.
+        """
+        search_lower = query_str.lower()
+        return (
+            self.db.query(Tag, Artifact, Package.name, Project.name)
+            .join(Artifact, Tag.artifact_id == Artifact.id)
+            .join(Package, Tag.package_id == Package.id)
+            .join(Project, Package.project_id == Project.id)
+            .filter(
+                or_(
+                    func.lower(Tag.name).contains(search_lower),
+                    func.lower(Artifact.original_name).contains(search_lower)
+                )
+            )
+            .order_by(Tag.name)
+            .limit(limit)
+            .all()
+        )
+
+    def update_metadata(self, artifact: Artifact, metadata: dict) -> Artifact:
+        """Update or merge format metadata."""
+        if artifact.format_metadata:
+            artifact.format_metadata = {**artifact.format_metadata, **metadata}
+        else:
+            artifact.format_metadata = metadata
+        self.db.flush()
+        return artifact

backend/app/repositories/base.py

@@ -0,0 +1,96 @@
+"""
+Base repository class with common CRUD operations.
+"""
+
+from typing import TypeVar, Generic, Type, Optional, List, Any, Dict
+from sqlalchemy.orm import Session
+from sqlalchemy import func, asc, desc
+from uuid import UUID
+
+from ..models import Base
+
+T = TypeVar("T", bound=Base)
+
+
+class BaseRepository(Generic[T]):
+    """
+    Base repository providing common CRUD operations.
+
+    Subclasses should set `model` class attribute to the SQLAlchemy model.
+    """
+
+    model: Type[T]
+
+    def __init__(self, db: Session):
+        self.db = db
+
+    def get_by_id(self, id: Any) -> Optional[T]:
+        """Get entity by primary key."""
+        return self.db.query(self.model).filter(self.model.id == id).first()
+
+    def get_all(
+        self,
+        skip: int = 0,
+        limit: int = 100,
+        order_by: str = None,
+        order_desc: bool = False,
+    ) -> List[T]:
+        """Get all entities with pagination and optional ordering."""
+        query = self.db.query(self.model)
+
+        if order_by and hasattr(self.model, order_by):
+            column = getattr(self.model, order_by)
+            query = query.order_by(desc(column) if order_desc else asc(column))
+
+        return query.offset(skip).limit(limit).all()
+
+    def count(self) -> int:
+        """Count total entities."""
+        return self.db.query(func.count(self.model.id)).scalar() or 0
+
+    def create(self, **kwargs) -> T:
+        """Create a new entity."""
+        entity = self.model(**kwargs)
+        self.db.add(entity)
+        self.db.flush()  # Flush to get ID without committing
+        return entity
+
+    def update(self, entity: T, **kwargs) -> T:
+        """Update an existing entity."""
+        for key, value in kwargs.items():
+            if hasattr(entity, key):
+                setattr(entity, key, value)
+        self.db.flush()
+        return entity
+
+    def delete(self, entity: T) -> None:
+        """Delete an entity."""
+        self.db.delete(entity)
+        self.db.flush()
+
+    def delete_by_id(self, id: Any) -> bool:
+        """Delete entity by ID. Returns True if deleted, False if not found."""
+        entity = self.get_by_id(id)
+        if entity:
+            self.delete(entity)
+            return True
+        return False
+
+    def exists(self, id: Any) -> bool:
+        """Check if entity exists by ID."""
+        return self.db.query(
+            self.db.query(self.model).filter(self.model.id == id).exists()
+        ).scalar()
+
+    def commit(self) -> None:
+        """Commit the current transaction."""
+        self.db.commit()
+
+    def rollback(self) -> None:
+        """Rollback the current transaction."""
+        self.db.rollback()
+
+    def refresh(self, entity: T) -> T:
+        """Refresh entity from database."""
+        self.db.refresh(entity)
+        return entity

backend/app/repositories/package.py

@@ -0,0 +1,177 @@
+"""
+Package repository for data access operations.
+"""
+
+from typing import Optional, List, Tuple
+from sqlalchemy.orm import Session
+from sqlalchemy import func, or_, asc, desc
+from uuid import UUID
+
+from .base import BaseRepository
+from ..models import Package, Project, Tag, Upload, Artifact
+
+
+class PackageRepository(BaseRepository[Package]):
+    """Repository for Package entity operations."""
+
+    model = Package
+
+    def get_by_name(self, project_id: UUID, name: str) -> Optional[Package]:
+        """Get package by name within a project."""
+        return (
+            self.db.query(Package)
+            .filter(Package.project_id == project_id, Package.name == name)
+            .first()
+        )
+
+    def get_by_project_and_name(self, project_name: str, package_name: str) -> Optional[Package]:
+        """Get package by project name and package name."""
+        return (
+            self.db.query(Package)
+            .join(Project, Package.project_id == Project.id)
+            .filter(Project.name == project_name, Package.name == package_name)
+            .first()
+        )
+
+    def exists_by_name(self, project_id: UUID, name: str) -> bool:
+        """Check if package with name exists in project."""
+        return self.db.query(
+            self.db.query(Package)
+            .filter(Package.project_id == project_id, Package.name == name)
+            .exists()
+        ).scalar()
+
+    def list_by_project(
+        self,
+        project_id: UUID,
+        page: int = 1,
+        limit: int = 20,
+        search: Optional[str] = None,
+        format: Optional[str] = None,
+        platform: Optional[str] = None,
+        sort: str = "name",
+        order: str = "asc",
+    ) -> Tuple[List[Package], int]:
+        """
+        List packages in a project with filtering and pagination.
+
+        Returns tuple of (packages, total_count).
+        """
+        query = self.db.query(Package).filter(Package.project_id == project_id)
+
+        # Apply search filter
+        if search:
+            search_lower = search.lower()
+            query = query.filter(
+                or_(
+                    func.lower(Package.name).contains(search_lower),
+                    func.lower(Package.description).contains(search_lower)
+                )
+            )
+
+        # Apply format filter
+        if format:
+            query = query.filter(Package.format == format)
+
+        # Apply platform filter
+        if platform:
+            query = query.filter(Package.platform == platform)
+
+        # Get total count
+        total = query.count()
+
+        # Apply sorting
+        sort_columns = {
+            "name": Package.name,
+            "created_at": Package.created_at,
+            "updated_at": Package.updated_at,
+        }
+        sort_column = sort_columns.get(sort, Package.name)
+        if order == "desc":
+            query = query.order_by(desc(sort_column))
+        else:
+            query = query.order_by(asc(sort_column))
+
+        # Apply pagination
+        offset = (page - 1) * limit
+        packages = query.offset(offset).limit(limit).all()
+
+        return packages, total
+
+    def create_package(
+        self,
+        project_id: UUID,
+        name: str,
+        description: Optional[str] = None,
+        format: str = "generic",
+        platform: str = "any",
+    ) -> Package:
+        """Create a new package."""
+        return self.create(
+            project_id=project_id,
+            name=name,
+            description=description,
+            format=format,
+            platform=platform,
+        )
+
+    def update_package(
+        self,
+        package: Package,
+        name: Optional[str] = None,
+        description: Optional[str] = None,
+        format: Optional[str] = None,
+        platform: Optional[str] = None,
+    ) -> Package:
+        """Update package fields."""
+        updates = {}
+        if name is not None:
+            updates["name"] = name
+        if description is not None:
+            updates["description"] = description
+        if format is not None:
+            updates["format"] = format
+        if platform is not None:
+            updates["platform"] = platform
+        return self.update(package, **updates)
+
+    def get_stats(self, package_id: UUID) -> dict:
+        """Get package statistics (tag count, artifact count, total size)."""
+        tag_count = (
+            self.db.query(func.count(Tag.id))
+            .filter(Tag.package_id == package_id)
+            .scalar() or 0
+        )
+
+        artifact_stats = (
+            self.db.query(
+                func.count(func.distinct(Upload.artifact_id)),
+                func.coalesce(func.sum(Artifact.size), 0)
+            )
+            .join(Artifact, Upload.artifact_id == Artifact.id)
+            .filter(Upload.package_id == package_id)
+            .first()
+        )
+
+        return {
+            "tag_count": tag_count,
+            "artifact_count": artifact_stats[0] if artifact_stats else 0,
+            "total_size": artifact_stats[1] if artifact_stats else 0,
+        }
+
+    def search(self, query_str: str, limit: int = 10) -> List[Tuple[Package, str]]:
+        """Search packages by name or description. Returns (package, project_name) tuples."""
+        search_lower = query_str.lower()
+        return (
+            self.db.query(Package, Project.name)
+            .join(Project, Package.project_id == Project.id)
+            .filter(
+                or_(
+                    func.lower(Package.name).contains(search_lower),
+                    func.lower(Package.description).contains(search_lower)
+                )
+            )
+            .order_by(Package.name)
+            .limit(limit)
+            .all()
+        )

backend/app/repositories/project.py

@@ -0,0 +1,132 @@
+"""
+Project repository for data access operations.
+"""
+
+from typing import Optional, List, Tuple
+from sqlalchemy.orm import Session
+from sqlalchemy import func, or_, asc, desc
+from uuid import UUID
+
+from .base import BaseRepository
+from ..models import Project
+
+
+class ProjectRepository(BaseRepository[Project]):
+    """Repository for Project entity operations."""
+
+    model = Project
+
+    def get_by_name(self, name: str) -> Optional[Project]:
+        """Get project by unique name."""
+        return self.db.query(Project).filter(Project.name == name).first()
+
+    def exists_by_name(self, name: str) -> bool:
+        """Check if project with name exists."""
+        return self.db.query(
+            self.db.query(Project).filter(Project.name == name).exists()
+        ).scalar()
+
+    def list_accessible(
+        self,
+        user_id: str,
+        page: int = 1,
+        limit: int = 20,
+        search: Optional[str] = None,
+        visibility: Optional[str] = None,
+        sort: str = "name",
+        order: str = "asc",
+    ) -> Tuple[List[Project], int]:
+        """
+        List projects accessible to user with filtering and pagination.
+
+        Returns tuple of (projects, total_count).
+        """
+        # Base query - filter by access
+        query = self.db.query(Project).filter(
+            or_(Project.is_public == True, Project.created_by == user_id)
+        )
+
+        # Apply visibility filter
+        if visibility == "public":
+            query = query.filter(Project.is_public == True)
+        elif visibility == "private":
+            query = query.filter(Project.is_public == False, Project.created_by == user_id)
+
+        # Apply search filter
+        if search:
+            search_lower = search.lower()
+            query = query.filter(
+                or_(
+                    func.lower(Project.name).contains(search_lower),
+                    func.lower(Project.description).contains(search_lower)
+                )
+            )
+
+        # Get total count before pagination
+        total = query.count()
+
+        # Apply sorting
+        sort_columns = {
+            "name": Project.name,
+            "created_at": Project.created_at,
+            "updated_at": Project.updated_at,
+        }
+        sort_column = sort_columns.get(sort, Project.name)
+        if order == "desc":
+            query = query.order_by(desc(sort_column))
+        else:
+            query = query.order_by(asc(sort_column))
+
+        # Apply pagination
+        offset = (page - 1) * limit
+        projects = query.offset(offset).limit(limit).all()
+
+        return projects, total
+
+    def create_project(
+        self,
+        name: str,
+        created_by: str,
+        description: Optional[str] = None,
+        is_public: bool = True,
+    ) -> Project:
+        """Create a new project."""
+        return self.create(
+            name=name,
+            description=description,
+            is_public=is_public,
+            created_by=created_by,
+        )
+
+    def update_project(
+        self,
+        project: Project,
+        name: Optional[str] = None,
+        description: Optional[str] = None,
+        is_public: Optional[bool] = None,
+    ) -> Project:
+        """Update project fields."""
+        updates = {}
+        if name is not None:
+            updates["name"] = name
+        if description is not None:
+            updates["description"] = description
+        if is_public is not None:
+            updates["is_public"] = is_public
+        return self.update(project, **updates)
+
+    def search(self, query_str: str, limit: int = 10) -> List[Project]:
+        """Search projects by name or description."""
+        search_lower = query_str.lower()
+        return (
+            self.db.query(Project)
+            .filter(
+                or_(
+                    func.lower(Project.name).contains(search_lower),
+                    func.lower(Project.description).contains(search_lower)
+                )
+            )
+            .order_by(Project.name)
+            .limit(limit)
+            .all()
+        )

backend/app/repositories/tag.py

@@ -0,0 +1,168 @@
+"""
+Tag repository for data access operations.
+"""
+
+from typing import Optional, List, Tuple
+from sqlalchemy.orm import Session
+from sqlalchemy import func, or_, asc, desc
+from uuid import UUID
+
+from .base import BaseRepository
+from ..models import Tag, TagHistory, Artifact, Package, Project
+
+
+class TagRepository(BaseRepository[Tag]):
+    """Repository for Tag entity operations."""
+
+    model = Tag
+
+    def get_by_name(self, package_id: UUID, name: str) -> Optional[Tag]:
+        """Get tag by name within a package."""
+        return (
+            self.db.query(Tag)
+            .filter(Tag.package_id == package_id, Tag.name == name)
+            .first()
+        )
+
+    def get_with_artifact(self, package_id: UUID, name: str) -> Optional[Tuple[Tag, Artifact]]:
+        """Get tag with its artifact."""
+        return (
+            self.db.query(Tag, Artifact)
+            .join(Artifact, Tag.artifact_id == Artifact.id)
+            .filter(Tag.package_id == package_id, Tag.name == name)
+            .first()
+        )
+
+    def exists_by_name(self, package_id: UUID, name: str) -> bool:
+        """Check if tag with name exists in package."""
+        return self.db.query(
+            self.db.query(Tag)
+            .filter(Tag.package_id == package_id, Tag.name == name)
+            .exists()
+        ).scalar()
+
+    def list_by_package(
+        self,
+        package_id: UUID,
+        page: int = 1,
+        limit: int = 20,
+        search: Optional[str] = None,
+        sort: str = "name",
+        order: str = "asc",
+    ) -> Tuple[List[Tuple[Tag, Artifact]], int]:
+        """
+        List tags in a package with artifact metadata.
+
+        Returns tuple of ((tag, artifact) tuples, total_count).
+        """
+        query = (
+            self.db.query(Tag, Artifact)
+            .join(Artifact, Tag.artifact_id == Artifact.id)
+            .filter(Tag.package_id == package_id)
+        )
+
+        # Apply search filter (tag name or artifact original filename)
+        if search:
+            search_lower = search.lower()
+            query = query.filter(
+                or_(
+                    func.lower(Tag.name).contains(search_lower),
+                    func.lower(Artifact.original_name).contains(search_lower)
+                )
+            )
+
+        # Get total count
+        total = query.count()
+
+        # Apply sorting
+        sort_columns = {
+            "name": Tag.name,
+            "created_at": Tag.created_at,
+        }
+        sort_column = sort_columns.get(sort, Tag.name)
+        if order == "desc":
+            query = query.order_by(desc(sort_column))
+        else:
+            query = query.order_by(asc(sort_column))
+
+        # Apply pagination
+        offset = (page - 1) * limit
+        results = query.offset(offset).limit(limit).all()
+
+        return results, total
+
+    def create_tag(
+        self,
+        package_id: UUID,
+        name: str,
+        artifact_id: str,
+        created_by: str,
+    ) -> Tag:
+        """Create a new tag."""
+        return self.create(
+            package_id=package_id,
+            name=name,
+            artifact_id=artifact_id,
+            created_by=created_by,
+        )
+
+    def update_artifact(
+        self,
+        tag: Tag,
+        new_artifact_id: str,
+        changed_by: str,
+        record_history: bool = True,
+    ) -> Tag:
+        """
+        Update tag to point to a different artifact.
+        Optionally records change in tag history.
+        """
+        old_artifact_id = tag.artifact_id
+
+        if record_history and old_artifact_id != new_artifact_id:
+            history = TagHistory(
+                tag_id=tag.id,
+                old_artifact_id=old_artifact_id,
+                new_artifact_id=new_artifact_id,
+                changed_by=changed_by,
+            )
+            self.db.add(history)
+
+        tag.artifact_id = new_artifact_id
+        tag.created_by = changed_by
+        self.db.flush()
+        return tag
+
+    def get_history(self, tag_id: UUID) -> List[TagHistory]:
+        """Get tag change history."""
+        return (
+            self.db.query(TagHistory)
+            .filter(TagHistory.tag_id == tag_id)
+            .order_by(TagHistory.changed_at.desc())
+            .all()
+        )
+
+    def get_latest_in_package(self, package_id: UUID) -> Optional[Tag]:
+        """Get the most recently created/updated tag in a package."""
+        return (
+            self.db.query(Tag)
+            .filter(Tag.package_id == package_id)
+            .order_by(Tag.created_at.desc())
+            .first()
+        )
+
+    def get_by_artifact(self, artifact_id: str) -> List[Tag]:
+        """Get all tags pointing to an artifact."""
+        return (
+            self.db.query(Tag)
+            .filter(Tag.artifact_id == artifact_id)
+            .all()
+        )
+
+    def count_by_artifact(self, artifact_id: str) -> int:
+        """Count tags pointing to an artifact."""
+        return (
+            self.db.query(func.count(Tag.id))
+            .filter(Tag.artifact_id == artifact_id)
+            .scalar() or 0
+        )

backend/app/repositories/upload.py

@@ -0,0 +1,136 @@
+"""
+Upload repository for data access operations.
+"""
+
+from typing import Optional, List, Tuple
+from datetime import datetime
+from sqlalchemy.orm import Session
+from sqlalchemy import func, desc
+from uuid import UUID
+
+from .base import BaseRepository
+from ..models import Upload, Artifact, Package, Project
+
+
+class UploadRepository(BaseRepository[Upload]):
+    """Repository for Upload entity operations."""
+
+    model = Upload
+
+    def create_upload(
+        self,
+        artifact_id: str,
+        package_id: UUID,
+        uploaded_by: str,
+        original_name: Optional[str] = None,
+        source_ip: Optional[str] = None,
+    ) -> Upload:
+        """Record a new upload event."""
+        return self.create(
+            artifact_id=artifact_id,
+            package_id=package_id,
+            original_name=original_name,
+            uploaded_by=uploaded_by,
+            source_ip=source_ip,
+        )
+
+    def list_by_package(
+        self,
+        package_id: UUID,
+        page: int = 1,
+        limit: int = 20,
+    ) -> Tuple[List[Upload], int]:
+        """List uploads for a package with pagination."""
+        query = self.db.query(Upload).filter(Upload.package_id == package_id)
+
+        total = query.count()
+        offset = (page - 1) * limit
+        uploads = query.order_by(Upload.uploaded_at.desc()).offset(offset).limit(limit).all()
+
+        return uploads, total
+
+    def list_by_artifact(self, artifact_id: str) -> List[Upload]:
+        """List all uploads of a specific artifact."""
+        return (
+            self.db.query(Upload)
+            .filter(Upload.artifact_id == artifact_id)
+            .order_by(Upload.uploaded_at.desc())
+            .all()
+        )
+
+    def get_latest_for_package(self, package_id: UUID) -> Optional[Upload]:
+        """Get the most recent upload for a package."""
+        return (
+            self.db.query(Upload)
+            .filter(Upload.package_id == package_id)
+            .order_by(Upload.uploaded_at.desc())
+            .first()
+        )
+
+    def get_latest_timestamp(self, package_id: UUID) -> Optional[datetime]:
+        """Get timestamp of most recent upload for a package."""
+        result = (
+            self.db.query(func.max(Upload.uploaded_at))
+            .filter(Upload.package_id == package_id)
+            .scalar()
+        )
+        return result
+
+    def count_by_artifact(self, artifact_id: str) -> int:
+        """Count uploads of a specific artifact."""
+        return (
+            self.db.query(func.count(Upload.id))
+            .filter(Upload.artifact_id == artifact_id)
+            .scalar() or 0
+        )
+
+    def count_by_package(self, package_id: UUID) -> int:
+        """Count total uploads for a package."""
+        return (
+            self.db.query(func.count(Upload.id))
+            .filter(Upload.package_id == package_id)
+            .scalar() or 0
+        )
+
+    def get_distinct_artifacts_count(self, package_id: UUID) -> int:
+        """Count distinct artifacts uploaded to a package."""
+        return (
+            self.db.query(func.count(func.distinct(Upload.artifact_id)))
+            .filter(Upload.package_id == package_id)
+            .scalar() or 0
+        )
+
+    def get_uploads_by_user(
+        self,
+        user_id: str,
+        page: int = 1,
+        limit: int = 20,
+    ) -> Tuple[List[Upload], int]:
+        """List uploads by a specific user."""
+        query = self.db.query(Upload).filter(Upload.uploaded_by == user_id)
+
+        total = query.count()
+        offset = (page - 1) * limit
+        uploads = query.order_by(Upload.uploaded_at.desc()).offset(offset).limit(limit).all()
+
+        return uploads, total
+
+    def get_upload_stats(self, package_id: UUID) -> dict:
+        """Get upload statistics for a package."""
+        stats = (
+            self.db.query(
+                func.count(Upload.id),
+                func.count(func.distinct(Upload.artifact_id)),
+                func.min(Upload.uploaded_at),
+                func.max(Upload.uploaded_at),
+            )
+            .filter(Upload.package_id == package_id)
+            .first()
+        )
+
+        return {
+            "total_uploads": stats[0] if stats else 0,
+            "unique_artifacts": stats[1] if stats else 0,
+            "first_upload": stats[2] if stats else None,
+            "last_upload": stats[3] if stats else None,
+        }

backend/app/services/__init__.py

@@ -0,0 +1,9 @@
+"""
+Service layer for business logic.
+"""
+
+from .artifact_cleanup import ArtifactCleanupService
+
+__all__ = [
+    "ArtifactCleanupService",
+]

backend/app/services/artifact_cleanup.py

@@ -0,0 +1,181 @@
+"""
+Service for artifact reference counting and cleanup.
+"""
+
+from typing import List, Optional, Tuple
+from sqlalchemy.orm import Session
+import logging
+
+from ..models import Artifact, Tag, Upload, Package
+from ..repositories.artifact import ArtifactRepository
+from ..repositories.tag import TagRepository
+from ..storage import S3Storage
+
+logger = logging.getLogger(__name__)
+
+
+class ArtifactCleanupService:
+    """
+    Service for managing artifact reference counts and cleaning up orphaned artifacts.
+
+    Reference counting rules:
+    - ref_count starts at 1 when artifact is first uploaded
+    - ref_count increments when the same artifact is uploaded again (deduplication)
+    - ref_count decrements when a tag is deleted or updated to point elsewhere
+    - ref_count decrements when a package is deleted (for each tag pointing to artifact)
+    - When ref_count reaches 0, artifact is a candidate for deletion from S3
+    """
+
+    def __init__(self, db: Session, storage: Optional[S3Storage] = None):
+        self.db = db
+        self.storage = storage
+        self.artifact_repo = ArtifactRepository(db)
+        self.tag_repo = TagRepository(db)
+
+    def on_tag_deleted(self, artifact_id: str) -> Artifact:
+        """
+        Called when a tag is deleted.
+        Decrements ref_count for the artifact the tag was pointing to.
+        """
+        artifact = self.artifact_repo.get_by_sha256(artifact_id)
+        if artifact:
+            artifact = self.artifact_repo.decrement_ref_count(artifact)
+            logger.info(f"Decremented ref_count for artifact {artifact_id}: now {artifact.ref_count}")
+        return artifact
+
+    def on_tag_updated(self, old_artifact_id: str, new_artifact_id: str) -> Tuple[Optional[Artifact], Optional[Artifact]]:
+        """
+        Called when a tag is updated to point to a different artifact.
+        Decrements ref_count for old artifact, increments for new (if different).
+
+        Returns (old_artifact, new_artifact) tuple.
+        """
+        old_artifact = None
+        new_artifact = None
+
+        if old_artifact_id != new_artifact_id:
+            # Decrement old artifact ref_count
+            old_artifact = self.artifact_repo.get_by_sha256(old_artifact_id)
+            if old_artifact:
+                old_artifact = self.artifact_repo.decrement_ref_count(old_artifact)
+                logger.info(f"Decremented ref_count for old artifact {old_artifact_id}: now {old_artifact.ref_count}")
+
+            # Increment new artifact ref_count
+            new_artifact = self.artifact_repo.get_by_sha256(new_artifact_id)
+            if new_artifact:
+                new_artifact = self.artifact_repo.increment_ref_count(new_artifact)
+                logger.info(f"Incremented ref_count for new artifact {new_artifact_id}: now {new_artifact.ref_count}")
+
+        return old_artifact, new_artifact
+
+    def on_package_deleted(self, package_id) -> List[str]:
+        """
+        Called when a package is deleted.
+        Decrements ref_count for all artifacts that had tags in the package.
+
+        Returns list of artifact IDs that were affected.
+        """
+        # Get all tags in the package before deletion
+        tags = self.db.query(Tag).filter(Tag.package_id == package_id).all()
+
+        affected_artifacts = []
+        for tag in tags:
+            artifact = self.artifact_repo.get_by_sha256(tag.artifact_id)
+            if artifact:
+                self.artifact_repo.decrement_ref_count(artifact)
+                affected_artifacts.append(tag.artifact_id)
+                logger.info(f"Decremented ref_count for artifact {tag.artifact_id} (package delete)")
+
+        return affected_artifacts
+
+    def cleanup_orphaned_artifacts(self, batch_size: int = 100, dry_run: bool = False) -> List[str]:
+        """
+        Find and delete artifacts with ref_count = 0.
+
+        Args:
+            batch_size: Maximum number of artifacts to process
+            dry_run: If True, only report what would be deleted without actually deleting
+
+        Returns:
+            List of artifact IDs that were (or would be) deleted
+        """
+        orphaned = self.artifact_repo.get_orphaned_artifacts(limit=batch_size)
+
+        deleted_ids = []
+        for artifact in orphaned:
+            if dry_run:
+                logger.info(f"[DRY RUN] Would delete orphaned artifact: {artifact.id}")
+                deleted_ids.append(artifact.id)
+            else:
+                try:
+                    # Delete from S3 first
+                    if self.storage:
+                        self.storage.delete(artifact.s3_key)
+                        logger.info(f"Deleted artifact from S3: {artifact.s3_key}")
+
+                    # Then delete from database
+                    self.artifact_repo.delete(artifact)
+                    deleted_ids.append(artifact.id)
+                    logger.info(f"Deleted orphaned artifact from database: {artifact.id}")
+                except Exception as e:
+                    logger.error(f"Failed to delete artifact {artifact.id}: {e}")
+
+        if not dry_run and deleted_ids:
+            self.db.commit()
+
+        return deleted_ids
+
+    def get_orphaned_count(self) -> int:
+        """Get count of artifacts with ref_count = 0."""
+        from sqlalchemy import func
+        return (
+            self.db.query(func.count(Artifact.id))
+            .filter(Artifact.ref_count == 0)
+            .scalar() or 0
+        )
+
+    def verify_ref_counts(self, fix: bool = False) -> List[dict]:
+        """
+        Verify that ref_counts match actual tag references.
+
+        Args:
+            fix: If True, fix any mismatched ref_counts
+
+        Returns:
+            List of artifacts with mismatched ref_counts
+        """
+        from sqlalchemy import func
+
+        # Get actual tag counts per artifact
+        tag_counts = (
+            self.db.query(Tag.artifact_id, func.count(Tag.id).label("tag_count"))
+            .group_by(Tag.artifact_id)
+            .all()
+        )
+        tag_count_map = {artifact_id: count for artifact_id, count in tag_counts}
+
+        # Check all artifacts
+        artifacts = self.db.query(Artifact).all()
+        mismatches = []
+
+        for artifact in artifacts:
+            actual_count = tag_count_map.get(artifact.id, 0)
+            # ref_count should be at least 1 (initial upload) + additional uploads
+            # But tags are the primary reference, so we check against tag count
+
+            if artifact.ref_count < actual_count:
+                mismatch = {
+                    "artifact_id": artifact.id,
+                    "stored_ref_count": artifact.ref_count,
+                    "actual_tag_count": actual_count,
+                }
+                mismatches.append(mismatch)
+
+                if fix:
+                    artifact.ref_count = max(actual_count, 1)
+                    logger.warning(f"Fixed ref_count for artifact {artifact.id}: {mismatch['stored_ref_count']} -> {artifact.ref_count}")
+
+        if fix and mismatches:
+            self.db.commit()
+
+        return mismatches