Fix migrations to remove is_public and allow_public_internet from schema

- Update migration 017 to not include is_public column or index
- Update migration 018 to not include allow_public_internet column
- Make migration 020 a no-op (public sources no longer seeded)

CHANGELOG.md

@@ -6,32 +6,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
-### Added
-- Added transparent PyPI proxy implementing PEP 503 Simple API (#108)
-  - `GET /pypi/simple/` - package index (proxied from upstream)
-  - `GET /pypi/simple/{package}/` - version list with rewritten download links
-  - `GET /pypi/simple/{package}/{filename}` - download with automatic caching
-  - Allows `pip install --index-url https://orchard.../pypi/simple/ <package>`
-  - Artifacts cached on first access through configured upstream sources
-- Added `POST /api/v1/cache/resolve` endpoint to cache packages by coordinates instead of URL (#108)
-
-### Changed
-- Upstream sources table text is now centered under column headers (#108)
-- ENV badge now appears inline with source name instead of separate column (#108)
-- Test and Edit buttons now have more prominent button styling (#108)
-- Reduced footer padding for cleaner layout (#108)
-
-### Fixed
-- Fixed purge_seed_data crash when deleting access permissions - was comparing UUID to VARCHAR column (#107)
-
 ### Changed
 - Upstream source connectivity test no longer follows redirects, fixing "Exceeded maximum allowed redirects" error with Artifactory proxies (#107)
+- Upstream sources table now has dedicated "Test" column with OK/Error status badges (#107)
 - Test runs automatically after saving a new or updated upstream source (#107)
-- Test status now shows as colored dots (green=success, red=error) instead of text badges (#107)
-- Clicking red dot shows error details in a modal (#107)
+- Error states in upstream sources table are now clickable to show full error details in a modal (#107)
 - Source name column no longer wraps text for better table layout (#107)
-- Renamed "Cache Management" page to "Upstream Sources" (#107)
-- Moved Delete button from table row to edit modal for cleaner table layout (#107)
 
 ### Removed
 - Removed `is_public` field from upstream sources - all sources are now treated as internal/private (#107)
@@ -39,8 +19,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Removed seeding of public registry URLs (npm-public, pypi-public, maven-central, docker-hub) (#107)
 - Removed "Public" badge and checkbox from upstream sources UI (#107)
 - Removed "Allow Public Internet" toggle from cache settings UI (#107)
-- Removed "Global Settings" section from cache management UI - auto-create system projects is always enabled (#107)
-- Removed unused CacheSettings frontend types and API functions (#107)
 
 ### Added
 - Added `ORCHARD_PURGE_SEED_DATA` environment variable support to stage helm values to remove seed data from long-running deployments (#107)

backend/app/config.py

@@ -64,11 +64,6 @@ class Settings(BaseSettings):
     # Global cache settings override (None = use DB value, True/False = override DB)
     cache_auto_create_system_projects: Optional[bool] = None  # Override auto_create_system_projects
 
-    # PyPI Cache Worker settings
-    pypi_cache_workers: int = 5  # Number of concurrent cache workers
-    pypi_cache_max_depth: int = 10  # Maximum recursion depth for dependency caching
-    pypi_cache_max_attempts: int = 3  # Maximum retry attempts for failed cache tasks
-
     # JWT Authentication settings (optional, for external identity providers)
     jwt_enabled: bool = False  # Enable JWT token validation
     jwt_secret: str = ""  # Secret key for HS256, or leave empty for RS256 with JWKS
@@ -93,24 +88,6 @@ class Settings(BaseSettings):
     def is_production(self) -> bool:
         return self.env.lower() == "production"
 
-    @property
-    def PORT(self) -> int:
-        """Alias for server_port for compatibility."""
-        return self.server_port
-
-    # Uppercase aliases for PyPI cache settings (for backward compatibility)
-    @property
-    def PYPI_CACHE_WORKERS(self) -> int:
-        return self.pypi_cache_workers
-
-    @property
-    def PYPI_CACHE_MAX_DEPTH(self) -> int:
-        return self.pypi_cache_max_depth
-
-    @property
-    def PYPI_CACHE_MAX_ATTEMPTS(self) -> int:
-        return self.pypi_cache_max_attempts
-
     class Config:
         env_prefix = "ORCHARD_"
         case_sensitive = False

backend/app/dependencies.py

@@ -10,20 +10,11 @@ Handles:
 - Conflict detection
 """
 
-import re
 import yaml
 from typing import List, Dict, Any, Optional, Set, Tuple
 from sqlalchemy.orm import Session
 from sqlalchemy import and_
 
-# Import packaging for PEP 440 version matching
-try:
-    from packaging.specifiers import SpecifierSet, InvalidSpecifier
-    from packaging.version import Version, InvalidVersion
-    HAS_PACKAGING = True
-except ImportError:
-    HAS_PACKAGING = False
-
 from .models import (
     Project,
     Package,
@@ -42,7 +33,6 @@ from .schemas import (
     ResolvedArtifact,
     DependencyResolutionResponse,
     DependencyConflict,
-    MissingDependency,
     PaginationMeta,
 )
 
@@ -314,95 +304,6 @@ def get_reverse_dependencies(
     )
 
 
-def _is_version_constraint(version_str: str) -> bool:
-    """Check if a version string contains constraint operators."""
-    if not version_str:
-        return False
-    # Check for common constraint operators
-    return any(op in version_str for op in ['>=', '<=', '!=', '~=', '>', '<', '==', '*'])
-
-
-def _resolve_version_constraint(
-    db: Session,
-    package: Package,
-    constraint: str,
-) -> Optional[Tuple[str, str, int]]:
-    """
-    Resolve a version constraint (e.g., '>=1.9') to a specific version.
-
-    Uses PEP 440 version matching to find the best matching version.
-
-    Args:
-        db: Database session
-        package: Package to search versions in
-        constraint: Version constraint string (e.g., '>=1.9', '<2.0,>=1.5')
-
-    Returns:
-        Tuple of (artifact_id, resolved_version, size) or None if not found
-    """
-    if not HAS_PACKAGING:
-        # Fallback: if packaging not available, can't do constraint matching
-        return None
-
-    # Handle wildcard - return latest version
-    if constraint == '*':
-        # Get the latest version by created_at
-        latest = db.query(PackageVersion).filter(
-            PackageVersion.package_id == package.id,
-        ).order_by(PackageVersion.created_at.desc()).first()
-        if latest:
-            artifact = db.query(Artifact).filter(Artifact.id == latest.artifact_id).first()
-            if artifact:
-                return (artifact.id, latest.version, artifact.size)
-        return None
-
-    try:
-        specifier = SpecifierSet(constraint)
-    except InvalidSpecifier:
-        # Invalid constraint (e.g., ">=" without version) - treat as wildcard
-        # This can happen with malformed metadata from PyPI packages
-        latest = db.query(PackageVersion).filter(
-            PackageVersion.package_id == package.id,
-        ).order_by(PackageVersion.created_at.desc()).first()
-        if latest:
-            artifact = db.query(Artifact).filter(Artifact.id == latest.artifact_id).first()
-            if artifact:
-                return (artifact.id, latest.version, artifact.size)
-        return None
-
-    # Get all versions for this package
-    all_versions = db.query(PackageVersion).filter(
-        PackageVersion.package_id == package.id,
-    ).all()
-
-    if not all_versions:
-        return None
-
-    # Find matching versions
-    matching = []
-    for pv in all_versions:
-        try:
-            v = Version(pv.version)
-            if v in specifier:
-                matching.append((pv, v))
-        except InvalidVersion:
-            # Skip invalid versions
-            continue
-
-    if not matching:
-        return None
-
-    # Sort by version (descending) and return the latest matching
-    matching.sort(key=lambda x: x[1], reverse=True)
-    best_match = matching[0][0]
-
-    artifact = db.query(Artifact).filter(Artifact.id == best_match.artifact_id).first()
-    if artifact:
-        return (artifact.id, best_match.version, artifact.size)
-
-    return None
-
-
 def _resolve_dependency_to_artifact(
     db: Session,
     project_name: str,
@@ -413,17 +314,11 @@ def _resolve_dependency_to_artifact(
     """
     Resolve a dependency constraint to an artifact ID.
 
-    Supports:
-    - Exact version matching (e.g., '1.2.3')
-    - Version constraints (e.g., '>=1.9', '<2.0,>=1.5')
-    - Tag matching
-    - Wildcard ('*' for any version)
-
     Args:
         db: Database session
         project_name: Project name
         package_name: Package name
-        version: Version or version constraint
+        version: Version constraint (exact)
         tag: Tag constraint
 
     Returns:
@@ -442,23 +337,17 @@ def _resolve_dependency_to_artifact(
         return None
 
     if version:
-        # Check if this is a version constraint (>=, <, etc.) or exact version
-        if _is_version_constraint(version):
-            result = _resolve_version_constraint(db, package, version)
-            if result:
-                return result
-        else:
-            # Look up by exact version
-            pkg_version = db.query(PackageVersion).filter(
-                PackageVersion.package_id == package.id,
-                PackageVersion.version == version,
+        # Look up by version
+        pkg_version = db.query(PackageVersion).filter(
+            PackageVersion.package_id == package.id,
+            PackageVersion.version == version,
+        ).first()
+        if pkg_version:
+            artifact = db.query(Artifact).filter(
+                Artifact.id == pkg_version.artifact_id
             ).first()
-            if pkg_version:
-                artifact = db.query(Artifact).filter(
-                    Artifact.id == pkg_version.artifact_id
-                ).first()
-                if artifact:
-                    return (artifact.id, version, artifact.size)
+            if artifact:
+                return (artifact.id, version, artifact.size)
 
         # Also check if there's a tag with this exact name
         tag_record = db.query(Tag).filter(
@@ -691,15 +580,11 @@ def resolve_dependencies(
 
     # Track resolved artifacts and their versions
     resolved_artifacts: Dict[str, ResolvedArtifact] = {}
-    # Track missing dependencies (not cached on server)
-    missing_dependencies: List[MissingDependency] = []
     # Track version requirements for conflict detection
     version_requirements: Dict[str, List[Dict[str, Any]]] = {}  # pkg_key -> [(version, required_by)]
     # Track visiting/visited for cycle detection
     visiting: Set[str] = set()
     visited: Set[str] = set()
-    # Track the current path for cycle reporting (artifact_id -> pkg_key)
-    current_path: Dict[str, str] = {}
     # Resolution order (topological)
     resolution_order: List[str] = []
 
@@ -721,10 +606,8 @@ def resolve_dependencies(
 
         # Cycle detection (at artifact level)
         if artifact_id in visiting:
-            # Build cycle path from current_path
-            cycle_start = current_path.get(artifact_id, pkg_key)
-            cycle = [cycle_start, pkg_key]
-            raise CircularDependencyError(cycle)
+            # Build cycle path
+            raise CircularDependencyError([pkg_key, pkg_key])
 
         # Conflict detection - check if we've seen this package before with a different version
         if pkg_key in version_requirements:
@@ -755,7 +638,6 @@ def resolve_dependencies(
             return
 
         visiting.add(artifact_id)
-        current_path[artifact_id] = pkg_key
 
         # Track version requirement
         if pkg_key not in version_requirements:
@@ -772,10 +654,6 @@ def resolve_dependencies(
 
         # Resolve each dependency first (depth-first)
         for dep in deps:
-            # Skip self-dependencies (can happen with PyPI extras like pytest[testing])
-            if dep.dependency_project == proj_name and dep.dependency_package == pkg_name:
-                continue
-
             resolved_dep = _resolve_dependency_to_artifact(
                 db,
                 dep.dependency_project,
@@ -785,22 +663,14 @@ def resolve_dependencies(
             )
 
             if not resolved_dep:
-                # Dependency not cached on server - track as missing but continue
                 constraint = dep.version_constraint or dep.tag_constraint
-                missing_dependencies.append(MissingDependency(
-                    project=dep.dependency_project,
-                    package=dep.dependency_package,
-                    constraint=constraint,
-                    required_by=pkg_key,
-                ))
-                continue
+                raise DependencyNotFoundError(
+                    dep.dependency_project,
+                    dep.dependency_package,
+                    constraint,
+                )
 
             dep_artifact_id, dep_version, dep_size = resolved_dep
-
-            # Skip if resolved to same artifact (self-dependency at artifact level)
-            if dep_artifact_id == artifact_id:
-                continue
-
             _resolve_recursive(
                 dep_artifact_id,
                 dep.dependency_project,
@@ -812,7 +682,6 @@ def resolve_dependencies(
             )
 
         visiting.remove(artifact_id)
-        del current_path[artifact_id]
         visited.add(artifact_id)
 
         # Add to resolution order (dependencies before dependents)
@@ -849,7 +718,6 @@ def resolve_dependencies(
             "ref": ref,
         },
         resolved=resolved_list,
-        missing=missing_dependencies,
         total_size=total_size,
         artifact_count=len(resolved_list),
     )

backend/app/main.py

@@ -11,7 +11,6 @@ from slowapi.errors import RateLimitExceeded
 from .config import get_settings
 from .database import init_db, SessionLocal
 from .routes import router
-from .pypi_proxy import router as pypi_router
 from .seed import seed_database
 from .auth import create_default_admin
 from .rate_limit import limiter
@@ -50,6 +49,7 @@ async def lifespan(app: FastAPI):
         logger.info(f"Running in {settings.env} mode - skipping seed data")
 
     yield
+    # Shutdown: cleanup if needed
 
 
 app = FastAPI(
@@ -65,7 +65,6 @@ app.add_exception_handler(RateLimitExceeded, _rate_limit_exceeded_handler)
 
 # Include API routes
 app.include_router(router)
-app.include_router(pypi_router)
 
 # Serve static files (React build) if the directory exists
 static_dir = os.path.join(os.path.dirname(__file__), "..", "..", "frontend", "dist")

backend/app/purge_seed_data.py

@@ -194,8 +194,7 @@ def purge_seed_data(db: Session) -> dict:
             synchronize_session=False
         )
         # Delete any access permissions for this user
-        # Note: AccessPermission.user_id is VARCHAR (username), not UUID
-        db.query(AccessPermission).filter(AccessPermission.user_id == user.username).delete(
+        db.query(AccessPermission).filter(AccessPermission.user_id == user.id).delete(
             synchronize_session=False
         )
         db.delete(user)

backend/app/pypi_proxy.py

@@ -1,642 +0,0 @@
-"""
-Transparent PyPI proxy implementing PEP 503 (Simple API).
-
-Provides endpoints that allow pip to use Orchard as a PyPI index URL.
-Artifacts are cached on first access through configured upstream sources.
-"""
-
-import hashlib
-import logging
-import os
-import re
-import tempfile
-from typing import Optional
-from urllib.parse import urljoin, urlparse, quote, unquote
-
-import httpx
-from fastapi import APIRouter, Depends, HTTPException, Request, Response
-from fastapi.responses import StreamingResponse, HTMLResponse
-from sqlalchemy.orm import Session
-
-from .database import get_db
-from .models import UpstreamSource, CachedUrl, Artifact, Project, Package, Tag, PackageVersion
-from .storage import S3Storage, get_storage
-from .config import get_env_upstream_sources
-
-logger = logging.getLogger(__name__)
-
-router = APIRouter(prefix="/pypi", tags=["pypi-proxy"])
-
-
-# Timeout configuration for proxy requests
-PROXY_CONNECT_TIMEOUT = 30.0
-PROXY_READ_TIMEOUT = 60.0
-
-
-def _extract_pypi_version(filename: str) -> Optional[str]:
-    """Extract version from PyPI filename.
-
-    Handles formats like:
-    - cowsay-6.1-py3-none-any.whl
-    - cowsay-1.0.tar.gz
-    - some_package-1.2.3.post1-cp39-cp39-linux_x86_64.whl
-    """
-    # Remove extension
-    if filename.endswith('.whl'):
-        # Wheel: name-version-pytag-abitag-platform.whl
-        parts = filename[:-4].split('-')
-        if len(parts) >= 2:
-            return parts[1]
-    elif filename.endswith('.tar.gz'):
-        # Source: name-version.tar.gz
-        base = filename[:-7]
-        # Find the last hyphen that precedes a version-like string
-        match = re.match(r'^(.+)-(\d+.*)$', base)
-        if match:
-            return match.group(2)
-    elif filename.endswith('.zip'):
-        # Egg/zip: name-version.zip
-        base = filename[:-4]
-        match = re.match(r'^(.+)-(\d+.*)$', base)
-        if match:
-            return match.group(2)
-    return None
-
-
-def _get_pypi_upstream_sources(db: Session) -> list[UpstreamSource]:
-    """Get all enabled upstream sources configured for PyPI."""
-    # Get database sources
-    db_sources = (
-        db.query(UpstreamSource)
-        .filter(
-            UpstreamSource.source_type == "pypi",
-            UpstreamSource.enabled == True,
-        )
-        .order_by(UpstreamSource.priority)
-        .all()
-    )
-
-    # Get env sources
-    env_sources = [
-        s for s in get_env_upstream_sources()
-        if s.source_type == "pypi" and s.enabled
-    ]
-
-    # Combine and sort by priority
-    all_sources = list(db_sources) + list(env_sources)
-    return sorted(all_sources, key=lambda s: s.priority)
-
-
-def _build_auth_headers(source) -> dict:
-    """Build authentication headers for an upstream source."""
-    headers = {}
-
-    if hasattr(source, 'auth_type'):
-        if source.auth_type == "bearer":
-            password = source.get_password() if hasattr(source, 'get_password') else getattr(source, 'password', None)
-            if password:
-                headers["Authorization"] = f"Bearer {password}"
-        elif source.auth_type == "api_key":
-            custom_headers = source.get_headers() if hasattr(source, 'get_headers') else {}
-            if custom_headers:
-                headers.update(custom_headers)
-
-    return headers
-
-
-def _get_basic_auth(source) -> Optional[tuple[str, str]]:
-    """Get basic auth credentials if applicable."""
-    if hasattr(source, 'auth_type') and source.auth_type == "basic":
-        username = getattr(source, 'username', None)
-        if username:
-            password = source.get_password() if hasattr(source, 'get_password') else getattr(source, 'password', '')
-            return (username, password or '')
-    return None
-
-
-def _get_base_url(request: Request) -> str:
-    """
-    Get the external base URL, respecting X-Forwarded-Proto header.
-
-    When behind a reverse proxy that terminates SSL, the request.base_url
-    will show http:// even though the external URL is https://. This function
-    checks the X-Forwarded-Proto header to determine the correct scheme.
-    """
-    base_url = str(request.base_url).rstrip('/')
-
-    # Check for X-Forwarded-Proto header (set by reverse proxies)
-    forwarded_proto = request.headers.get('x-forwarded-proto')
-    if forwarded_proto:
-        # Replace the scheme with the forwarded protocol
-        parsed = urlparse(base_url)
-        base_url = f"{forwarded_proto}://{parsed.netloc}{parsed.path}"
-
-    return base_url
-
-
-def _rewrite_package_links(html: str, base_url: str, package_name: str, upstream_base_url: str) -> str:
-    """
-    Rewrite download links in a PyPI simple page to go through our proxy.
-
-    Args:
-        html: The HTML content from upstream
-        base_url: Our server's base URL
-        package_name: The package name for the URL path
-        upstream_base_url: The upstream URL used to fetch this page (for resolving relative URLs)
-
-    Returns:
-        HTML with rewritten download links
-    """
-    # Pattern to match href attributes in anchor tags
-    # PyPI simple pages have links like:
-    # <a href="https://files.pythonhosted.org/packages/.../file.tar.gz#sha256=...">file.tar.gz</a>
-    # Or relative URLs from Artifactory like:
-    # <a href="../../packages/packages/62/35/.../requests-0.10.0.tar.gz#sha256=...">
-
-    def replace_href(match):
-        original_url = match.group(1)
-
-        # Resolve relative URLs to absolute using the upstream base URL
-        if not original_url.startswith(('http://', 'https://')):
-            # Split off fragment before resolving
-            url_without_fragment = original_url.split('#')[0]
-            fragment_part = original_url[len(url_without_fragment):]
-            absolute_url = urljoin(upstream_base_url, url_without_fragment) + fragment_part
-        else:
-            absolute_url = original_url
-
-        # Extract the filename from the URL
-        parsed = urlparse(absolute_url)
-        path_parts = parsed.path.split('/')
-        filename = path_parts[-1] if path_parts else ''
-
-        # Keep the hash fragment if present
-        fragment = f"#{parsed.fragment}" if parsed.fragment else ""
-
-        # Encode the absolute URL (without fragment) for safe transmission
-        encoded_url = quote(absolute_url.split('#')[0], safe='')
-
-        # Build new URL pointing to our proxy
-        new_url = f"{base_url}/pypi/simple/{package_name}/{filename}?upstream={encoded_url}{fragment}"
-
-        return f'href="{new_url}"'
-
-    # Match href="..." patterns
-    rewritten = re.sub(r'href="([^"]+)"', replace_href, html)
-
-    return rewritten
-
-
-@router.get("/simple/")
-async def pypi_simple_index(
-    request: Request,
-    db: Session = Depends(get_db),
-):
-    """
-    PyPI Simple API index - lists all packages.
-
-    Proxies to the first available upstream PyPI source.
-    """
-    sources = _get_pypi_upstream_sources(db)
-
-    if not sources:
-        raise HTTPException(
-            status_code=503,
-            detail="No PyPI upstream sources configured"
-        )
-
-    # Try each source in priority order
-    last_error = None
-    for source in sources:
-        try:
-            headers = {"User-Agent": "Orchard-PyPI-Proxy/1.0"}
-            headers.update(_build_auth_headers(source))
-            auth = _get_basic_auth(source)
-
-            # Use URL as-is - users should provide full path including /simple
-            simple_url = source.url.rstrip('/') + '/'
-
-            timeout = httpx.Timeout(PROXY_READ_TIMEOUT, connect=PROXY_CONNECT_TIMEOUT)
-
-            async with httpx.AsyncClient(timeout=timeout, follow_redirects=False) as client:
-                response = await client.get(
-                    simple_url,
-                    headers=headers,
-                    auth=auth,
-                )
-
-                # Handle redirects manually to avoid loops
-                if response.status_code in (301, 302, 303, 307, 308):
-                    redirect_url = response.headers.get('location')
-                    if redirect_url:
-                        # Follow the redirect once
-                        response = await client.get(
-                            redirect_url,
-                            headers=headers,
-                            auth=auth,
-                            follow_redirects=False,
-                        )
-
-                if response.status_code == 200:
-                    # Return the index as-is (links are to package pages, not files)
-                    # We could rewrite these too, but for now just proxy
-                    content = response.text
-
-                    # Rewrite package links to go through our proxy
-                    base_url = _get_base_url(request)
-                    content = re.sub(
-                        r'href="([^"]+)/"',
-                        lambda m: f'href="{base_url}/pypi/simple/{m.group(1)}/"',
-                        content
-                    )
-
-                    return HTMLResponse(content=content)
-
-                last_error = f"HTTP {response.status_code}"
-
-        except httpx.ConnectError as e:
-            last_error = f"Connection failed: {e}"
-            logger.warning(f"PyPI proxy: failed to connect to {source.url}: {e}")
-        except httpx.TimeoutException as e:
-            last_error = f"Timeout: {e}"
-            logger.warning(f"PyPI proxy: timeout connecting to {source.url}: {e}")
-        except Exception as e:
-            last_error = str(e)
-            logger.warning(f"PyPI proxy: error fetching from {source.url}: {e}")
-
-    raise HTTPException(
-        status_code=502,
-        detail=f"Failed to fetch package index from upstream: {last_error}"
-    )
-
-
-@router.get("/simple/{package_name}/")
-async def pypi_package_versions(
-    request: Request,
-    package_name: str,
-    db: Session = Depends(get_db),
-):
-    """
-    PyPI Simple API package page - lists all versions/files for a package.
-
-    Proxies to upstream and rewrites download links to go through our cache.
-    """
-    sources = _get_pypi_upstream_sources(db)
-
-    if not sources:
-        raise HTTPException(
-            status_code=503,
-            detail="No PyPI upstream sources configured"
-        )
-
-    base_url = _get_base_url(request)
-
-    # Normalize package name (PEP 503)
-    normalized_name = re.sub(r'[-_.]+', '-', package_name).lower()
-
-    # Try each source in priority order
-    last_error = None
-    for source in sources:
-        try:
-            headers = {"User-Agent": "Orchard-PyPI-Proxy/1.0"}
-            headers.update(_build_auth_headers(source))
-            auth = _get_basic_auth(source)
-
-            # Use URL as-is - users should provide full path including /simple
-            package_url = source.url.rstrip('/') + f'/{normalized_name}/'
-            final_url = package_url  # Track final URL after redirects
-
-            timeout = httpx.Timeout(PROXY_READ_TIMEOUT, connect=PROXY_CONNECT_TIMEOUT)
-
-            async with httpx.AsyncClient(timeout=timeout, follow_redirects=False) as client:
-                response = await client.get(
-                    package_url,
-                    headers=headers,
-                    auth=auth,
-                )
-
-                # Handle redirects manually
-                redirect_count = 0
-                while response.status_code in (301, 302, 303, 307, 308) and redirect_count < 5:
-                    redirect_url = response.headers.get('location')
-                    if not redirect_url:
-                        break
-
-                    # Make redirect URL absolute if needed
-                    if not redirect_url.startswith('http'):
-                        redirect_url = urljoin(final_url, redirect_url)
-
-                    final_url = redirect_url  # Update final URL
-
-                    response = await client.get(
-                        redirect_url,
-                        headers=headers,
-                        auth=auth,
-                        follow_redirects=False,
-                    )
-                    redirect_count += 1
-
-                if response.status_code == 200:
-                    content = response.text
-
-                    # Rewrite download links to go through our proxy
-                    # Pass final_url so relative URLs can be resolved correctly
-                    content = _rewrite_package_links(content, base_url, normalized_name, final_url)
-
-                    return HTMLResponse(content=content)
-
-                if response.status_code == 404:
-                    # Package not found in this source, try next
-                    last_error = f"Package not found in {source.name}"
-                    continue
-
-                last_error = f"HTTP {response.status_code}"
-
-        except httpx.ConnectError as e:
-            last_error = f"Connection failed: {e}"
-            logger.warning(f"PyPI proxy: failed to connect to {source.url}: {e}")
-        except httpx.TimeoutException as e:
-            last_error = f"Timeout: {e}"
-            logger.warning(f"PyPI proxy: timeout connecting to {source.url}: {e}")
-        except Exception as e:
-            last_error = str(e)
-            logger.warning(f"PyPI proxy: error fetching {package_name} from {source.url}: {e}")
-
-    raise HTTPException(
-        status_code=404,
-        detail=f"Package '{package_name}' not found: {last_error}"
-    )
-
-
-@router.get("/simple/{package_name}/{filename}")
-async def pypi_download_file(
-    request: Request,
-    package_name: str,
-    filename: str,
-    upstream: Optional[str] = None,
-    db: Session = Depends(get_db),
-    storage: S3Storage = Depends(get_storage),
-):
-    """
-    Download a package file, caching it in Orchard.
-
-    Args:
-        package_name: The package name
-        filename: The filename to download
-        upstream: URL-encoded upstream URL to fetch from
-    """
-    if not upstream:
-        raise HTTPException(
-            status_code=400,
-            detail="Missing 'upstream' query parameter with source URL"
-        )
-
-    # Decode the upstream URL
-    upstream_url = unquote(upstream)
-
-    # Check if we already have this URL cached
-    url_hash = hashlib.sha256(upstream_url.encode()).hexdigest()
-    cached_url = db.query(CachedUrl).filter(CachedUrl.url_hash == url_hash).first()
-
-    if cached_url:
-        # Serve from cache
-        artifact = db.query(Artifact).filter(Artifact.id == cached_url.artifact_id).first()
-        if artifact:
-            logger.info(f"PyPI proxy: serving cached {filename} (artifact {artifact.id[:12]})")
-
-            # Stream from S3
-            try:
-                stream, content_length, _ = storage.get_stream(artifact.s3_key)
-
-                def stream_content():
-                    """Generator that yields chunks from the S3 stream."""
-                    try:
-                        for chunk in stream.iter_chunks():
-                            yield chunk
-                    finally:
-                        stream.close()
-
-                return StreamingResponse(
-                    stream_content(),
-                    media_type=artifact.content_type or "application/octet-stream",
-                    headers={
-                        "Content-Disposition": f'attachment; filename="{filename}"',
-                        "Content-Length": str(content_length),
-                        "X-Checksum-SHA256": artifact.id,
-                        "X-Cache": "HIT",
-                    }
-                )
-            except Exception as e:
-                logger.error(f"PyPI proxy: error streaming cached artifact: {e}")
-                # Fall through to fetch from upstream
-
-    # Not cached - fetch from upstream
-    sources = _get_pypi_upstream_sources(db)
-
-    # Use the first available source for authentication headers
-    # Note: The upstream URL may point to files.pythonhosted.org or other CDNs,
-    # not the configured source URL directly, so we can't strictly validate the host
-    matched_source = sources[0] if sources else None
-
-    try:
-        headers = {"User-Agent": "Orchard-PyPI-Proxy/1.0"}
-        if matched_source:
-            headers.update(_build_auth_headers(matched_source))
-        auth = _get_basic_auth(matched_source) if matched_source else None
-
-        timeout = httpx.Timeout(300.0, connect=PROXY_CONNECT_TIMEOUT)  # 5 minutes for large files
-
-        # Fetch the file
-        logger.info(f"PyPI proxy: fetching {filename} from {upstream_url}")
-
-        async with httpx.AsyncClient(timeout=timeout, follow_redirects=False) as client:
-            response = await client.get(
-                upstream_url,
-                headers=headers,
-                auth=auth,
-            )
-
-            # Handle redirects manually
-            redirect_count = 0
-            while response.status_code in (301, 302, 303, 307, 308) and redirect_count < 5:
-                redirect_url = response.headers.get('location')
-                if not redirect_url:
-                    break
-
-                if not redirect_url.startswith('http'):
-                    redirect_url = urljoin(upstream_url, redirect_url)
-
-                logger.info(f"PyPI proxy: following redirect to {redirect_url}")
-
-                # Don't send auth to different hosts
-                redirect_headers = {"User-Agent": "Orchard-PyPI-Proxy/1.0"}
-                redirect_auth = None
-                if urlparse(redirect_url).netloc == urlparse(upstream_url).netloc:
-                    redirect_headers.update(headers)
-                    redirect_auth = auth
-
-                response = await client.get(
-                    redirect_url,
-                    headers=redirect_headers,
-                    auth=redirect_auth,
-                    follow_redirects=False,
-                )
-                redirect_count += 1
-
-            if response.status_code != 200:
-                raise HTTPException(
-                    status_code=response.status_code,
-                    detail=f"Upstream returned {response.status_code}"
-                )
-
-            content_type = response.headers.get('content-type', 'application/octet-stream')
-
-            # Stream to temp file to avoid loading large packages into memory
-            # This keeps memory usage constant regardless of package size
-            # Using async iteration to avoid blocking the event loop
-            tmp_path = None
-            try:
-                with tempfile.NamedTemporaryFile(delete=False, suffix=f"_{filename}") as tmp_file:
-                    tmp_path = tmp_file.name
-                    async for chunk in response.aiter_bytes(chunk_size=65536):  # 64KB chunks
-                        tmp_file.write(chunk)
-
-                # Store in S3 from temp file (computes hash and deduplicates automatically)
-                with open(tmp_path, 'rb') as f:
-                    result = storage.store(f)
-                sha256 = result.sha256
-                size = result.size
-
-                # Read content for response
-                with open(tmp_path, 'rb') as f:
-                    content = f.read()
-
-                logger.info(f"PyPI proxy: downloaded {filename}, {size} bytes, sha256={sha256[:12]}")
-            finally:
-                # Clean up temp file
-                if tmp_path and os.path.exists(tmp_path):
-                    os.unlink(tmp_path)
-
-        # Check if artifact already exists
-        existing = db.query(Artifact).filter(Artifact.id == sha256).first()
-        if existing:
-            # Increment ref count
-            existing.ref_count += 1
-            db.flush()
-        else:
-            # Create artifact record
-            new_artifact = Artifact(
-                id=sha256,
-                original_name=filename,
-                content_type=content_type,
-                size=size,
-                ref_count=1,
-                created_by="pypi-proxy",
-                s3_key=result.s3_key,
-                checksum_md5=result.md5,
-                checksum_sha1=result.sha1,
-                s3_etag=result.s3_etag,
-            )
-            db.add(new_artifact)
-            db.flush()
-
-        # Create/get system project and package
-        system_project = db.query(Project).filter(Project.name == "_pypi").first()
-        if not system_project:
-            system_project = Project(
-                name="_pypi",
-                description="System project for cached PyPI packages",
-                is_public=True,
-                is_system=True,
-                created_by="pypi-proxy",
-            )
-            db.add(system_project)
-            db.flush()
-        elif not system_project.is_system:
-            # Ensure existing project is marked as system
-            system_project.is_system = True
-            db.flush()
-
-        # Normalize package name
-        normalized_name = re.sub(r'[-_.]+', '-', package_name).lower()
-
-        package = db.query(Package).filter(
-            Package.project_id == system_project.id,
-            Package.name == normalized_name,
-        ).first()
-        if not package:
-            package = Package(
-                project_id=system_project.id,
-                name=normalized_name,
-                description=f"PyPI package: {normalized_name}",
-                format="pypi",
-            )
-            db.add(package)
-            db.flush()
-
-        # Create tag with filename
-        existing_tag = db.query(Tag).filter(
-            Tag.package_id == package.id,
-            Tag.name == filename,
-        ).first()
-        if not existing_tag:
-            tag = Tag(
-                package_id=package.id,
-                name=filename,
-                artifact_id=sha256,
-                created_by="pypi-proxy",
-            )
-            db.add(tag)
-
-        # Extract and create version
-        # Only create version for actual package files, not .metadata files
-        version = _extract_pypi_version(filename)
-        if version and not filename.endswith('.metadata'):
-            # Check by version string (the unique constraint is on package_id + version)
-            existing_version = db.query(PackageVersion).filter(
-                PackageVersion.package_id == package.id,
-                PackageVersion.version == version,
-            ).first()
-            if not existing_version:
-                pkg_version = PackageVersion(
-                    package_id=package.id,
-                    artifact_id=sha256,
-                    version=version,
-                    version_source="filename",
-                    created_by="pypi-proxy",
-                )
-                db.add(pkg_version)
-
-        # Cache the URL mapping
-        existing_cached = db.query(CachedUrl).filter(CachedUrl.url_hash == url_hash).first()
-        if not existing_cached:
-            cached_url_record = CachedUrl(
-                url_hash=url_hash,
-                url=upstream_url,
-                artifact_id=sha256,
-            )
-            db.add(cached_url_record)
-
-        db.commit()
-
-        # Return the file
-        return Response(
-            content=content,
-            media_type=content_type,
-            headers={
-                "Content-Disposition": f'attachment; filename="{filename}"',
-                "Content-Length": str(size),
-                "X-Checksum-SHA256": sha256,
-                "X-Cache": "MISS",
-            }
-        )
-
-    except httpx.ConnectError as e:
-        raise HTTPException(status_code=502, detail=f"Connection failed: {e}")
-    except httpx.TimeoutException as e:
-        raise HTTPException(status_code=504, detail=f"Timeout: {e}")
-    except HTTPException:
-        raise
-    except Exception as e:
-        logger.exception(f"PyPI proxy: error downloading {filename}")
-        raise HTTPException(status_code=500, detail=str(e))

backend/app/routes.py

@@ -1680,7 +1680,6 @@ def create_project(
         name=db_project.name,
         description=db_project.description,
         is_public=db_project.is_public,
-        is_system=db_project.is_system,
         created_at=db_project.created_at,
         updated_at=db_project.updated_at,
         created_by=db_project.created_by,
@@ -1705,7 +1704,6 @@ def get_project(
         name=project.name,
         description=project.description,
         is_public=project.is_public,
-        is_system=project.is_system,
         created_at=project.created_at,
         updated_at=project.updated_at,
         created_by=project.created_by,
@@ -2706,7 +2704,6 @@ def list_team_projects(
                 name=p.name,
                 description=p.description,
                 is_public=p.is_public,
-                is_system=p.is_system,
                 created_at=p.created_at,
                 updated_at=p.updated_at,
                 created_by=p.created_by,
@@ -2830,15 +2827,14 @@ def list_packages(
             db.query(func.count(Tag.id)).filter(Tag.package_id == pkg.id).scalar() or 0
         )
 
-        # Get unique artifact count and total size via tags
-        # (PyPI proxy creates tags without uploads, so query from tags)
+        # Get unique artifact count and total size via uploads
         artifact_stats = (
             db.query(
-                func.count(func.distinct(Tag.artifact_id)),
+                func.count(func.distinct(Upload.artifact_id)),
                 func.coalesce(func.sum(Artifact.size), 0),
             )
-            .join(Artifact, Tag.artifact_id == Artifact.id)
-            .filter(Tag.package_id == pkg.id)
+            .join(Artifact, Upload.artifact_id == Artifact.id)
+            .filter(Upload.package_id == pkg.id)
             .first()
         )
         artifact_count = artifact_stats[0] if artifact_stats else 0
@@ -2934,15 +2930,14 @@ def get_package(
         db.query(func.count(Tag.id)).filter(Tag.package_id == pkg.id).scalar() or 0
     )
 
-    # Get unique artifact count and total size via tags
-    # (PyPI proxy creates tags without uploads, so query from tags)
+    # Get unique artifact count and total size via uploads
     artifact_stats = (
         db.query(
-            func.count(func.distinct(Tag.artifact_id)),
+            func.count(func.distinct(Upload.artifact_id)),
             func.coalesce(func.sum(Artifact.size), 0),
         )
-        .join(Artifact, Tag.artifact_id == Artifact.id)
-        .filter(Tag.package_id == pkg.id)
+        .join(Artifact, Upload.artifact_id == Artifact.id)
+        .filter(Upload.package_id == pkg.id)
         .first()
     )
     artifact_count = artifact_stats[0] if artifact_stats else 0
@@ -6285,14 +6280,14 @@ def get_package_stats(
         db.query(func.count(Tag.id)).filter(Tag.package_id == package.id).scalar() or 0
     )
 
-    # Artifact stats via tags (tags exist for both user uploads and PyPI proxy)
+    # Artifact stats via uploads
     artifact_stats = (
         db.query(
-            func.count(func.distinct(Tag.artifact_id)),
+            func.count(func.distinct(Upload.artifact_id)),
             func.coalesce(func.sum(Artifact.size), 0),
         )
-        .join(Artifact, Tag.artifact_id == Artifact.id)
-        .filter(Tag.package_id == package.id)
+        .join(Artifact, Upload.artifact_id == Artifact.id)
+        .filter(Upload.package_id == package.id)
         .first()
     )
     artifact_count = artifact_stats[0] if artifact_stats else 0
@@ -8310,200 +8305,6 @@ def _create_user_cache_reference(
     return f"{user_project_name}/{user_package_name}"
 
 
-# --- Cache Resolve Endpoint ---
-
-from .schemas import CacheResolveRequest
-
-
-@router.post(
-    "/api/v1/cache/resolve",
-    response_model=CacheResponse,
-    tags=["cache"],
-    summary="Cache an artifact by package coordinates",
-)
-def cache_resolve(
-    request: Request,
-    resolve_request: CacheResolveRequest,
-    db: Session = Depends(get_db),
-    storage: S3Storage = Depends(get_storage),
-    current_user: User = Depends(get_current_user),
-):
-    """
-    Cache an artifact by package coordinates (no URL required).
-
-    The server finds the appropriate download URL based on source_type
-    and configured upstream sources. Currently supports PyPI packages.
-
-    **Request Body:**
-    - `source_type` (required): Type of source (pypi, npm, maven, etc.)
-    - `package` (required): Package name
-    - `version` (required): Package version
-    - `user_project` (optional): Also create reference in this user project
-    - `user_package` (optional): Package name in user project
-    - `user_tag` (optional): Tag name in user project
-
-    **Example (curl):**
-    ```bash
-    curl -X POST "http://localhost:8080/api/v1/cache/resolve" \\
-      -H "Authorization: Bearer <api-key>" \\
-      -H "Content-Type: application/json" \\
-      -d '{
-        "source_type": "pypi",
-        "package": "requests",
-        "version": "2.31.0"
-      }'
-    ```
-    """
-    import re
-    import httpx
-    from urllib.parse import quote, unquote
-
-    if resolve_request.source_type != "pypi":
-        raise HTTPException(
-            status_code=501,
-            detail=f"Cache resolve for '{resolve_request.source_type}' not yet implemented. Currently only 'pypi' is supported."
-        )
-
-    # Get PyPI upstream sources
-    sources = (
-        db.query(UpstreamSource)
-        .filter(
-            UpstreamSource.source_type == "pypi",
-            UpstreamSource.enabled == True,
-        )
-        .order_by(UpstreamSource.priority)
-        .all()
-    )
-
-    # Also get env sources
-    env_sources = [
-        s for s in get_env_upstream_sources()
-        if s.source_type == "pypi" and s.enabled
-    ]
-    all_sources = list(sources) + list(env_sources)
-    all_sources = sorted(all_sources, key=lambda s: s.priority)
-
-    if not all_sources:
-        raise HTTPException(
-            status_code=503,
-            detail="No PyPI upstream sources configured"
-        )
-
-    # Normalize package name (PEP 503)
-    normalized_package = re.sub(r'[-_.]+', '-', resolve_request.package).lower()
-
-    # Query the Simple API to find the download URL
-    download_url = None
-    matched_filename = None
-    last_error = None
-
-    for source in all_sources:
-        try:
-            headers = {"User-Agent": "Orchard-CacheResolver/1.0"}
-
-            # Build auth if needed
-            if hasattr(source, 'auth_type'):
-                if source.auth_type == "bearer":
-                    password = source.get_password() if hasattr(source, 'get_password') else getattr(source, 'password', None)
-                    if password:
-                        headers["Authorization"] = f"Bearer {password}"
-                elif source.auth_type == "api_key":
-                    custom_headers = source.get_headers() if hasattr(source, 'get_headers') else {}
-                    if custom_headers:
-                        headers.update(custom_headers)
-
-            auth = None
-            if hasattr(source, 'auth_type') and source.auth_type == "basic":
-                username = getattr(source, 'username', None)
-                if username:
-                    password = source.get_password() if hasattr(source, 'get_password') else getattr(source, 'password', '')
-                    auth = (username, password or '')
-
-            source_url = getattr(source, 'url', '')
-            package_url = source_url.rstrip('/') + f'/simple/{normalized_package}/'
-
-            timeout = httpx.Timeout(connect=30.0, read=60.0)
-
-            with httpx.Client(timeout=timeout, follow_redirects=True) as client:
-                response = client.get(package_url, headers=headers, auth=auth)
-
-                if response.status_code == 404:
-                    last_error = f"Package not found in {getattr(source, 'name', 'source')}"
-                    continue
-
-                if response.status_code != 200:
-                    last_error = f"HTTP {response.status_code} from {getattr(source, 'name', 'source')}"
-                    continue
-
-                # Parse HTML to find the version
-                html = response.text
-                # Look for links containing the version
-                # Pattern: href="...{package}-{version}...#sha256=..."
-                version_pattern = re.escape(resolve_request.version)
-                link_pattern = rf'href="([^"]+{normalized_package}[^"]*{version_pattern}[^"]*)"'
-
-                matches = re.findall(link_pattern, html, re.IGNORECASE)
-
-                if not matches:
-                    # Try with original package name
-                    link_pattern = rf'href="([^"]+{re.escape(resolve_request.package)}[^"]*{version_pattern}[^"]*)"'
-                    matches = re.findall(link_pattern, html, re.IGNORECASE)
-
-                if matches:
-                    # Prefer .tar.gz or .whl files
-                    for match in matches:
-                        url = match.split('#')[0]  # Remove hash fragment
-                        if url.endswith('.tar.gz') or url.endswith('.whl'):
-                            download_url = url
-                            # Extract filename
-                            matched_filename = url.split('/')[-1]
-                            break
-                    if not download_url:
-                        # Use first match
-                        download_url = matches[0].split('#')[0]
-                        matched_filename = download_url.split('/')[-1]
-                    break
-
-                last_error = f"Version {resolve_request.version} not found for {resolve_request.package}"
-
-        except httpx.ConnectError as e:
-            last_error = f"Connection failed: {e}"
-            logger.warning(f"Cache resolve: failed to connect to {getattr(source, 'url', 'source')}: {e}")
-        except httpx.TimeoutException as e:
-            last_error = f"Timeout: {e}"
-            logger.warning(f"Cache resolve: timeout connecting to {getattr(source, 'url', 'source')}: {e}")
-        except Exception as e:
-            last_error = str(e)
-            logger.warning(f"Cache resolve: error: {e}")
-
-    if not download_url:
-        raise HTTPException(
-            status_code=404,
-            detail=f"Could not find {resolve_request.package}=={resolve_request.version}: {last_error}"
-        )
-
-    # Now cache the artifact using the existing cache_artifact logic
-    # Construct a CacheRequest
-    cache_request = CacheRequest(
-        url=download_url,
-        source_type="pypi",
-        package_name=normalized_package,
-        tag=matched_filename or resolve_request.version,
-        user_project=resolve_request.user_project,
-        user_package=resolve_request.user_package,
-        user_tag=resolve_request.user_tag,
-    )
-
-    # Call the cache logic
-    return cache_artifact(
-        request=request,
-        cache_request=cache_request,
-        db=db,
-        storage=storage,
-        current_user=current_user,
-    )
-
-
 # --- Upstream Sources Admin API ---
 
 from .schemas import (

backend/app/schemas.py

@@ -33,7 +33,6 @@ class ProjectResponse(BaseModel):
     name: str
     description: Optional[str]
     is_public: bool
-    is_system: bool = False
     created_at: datetime
     updated_at: datetime
     created_by: str
@@ -1033,19 +1032,10 @@ class ResolvedArtifact(BaseModel):
     download_url: str
 
 
-class MissingDependency(BaseModel):
-    """A dependency that could not be resolved (not cached on server)"""
-    project: str
-    package: str
-    constraint: Optional[str] = None
-    required_by: Optional[str] = None
-
-
 class DependencyResolutionResponse(BaseModel):
     """Response from dependency resolution endpoint"""
     requested: Dict[str, str]  # project, package, ref
     resolved: List[ResolvedArtifact]
-    missing: List[MissingDependency] = []
     total_size: int
     artifact_count: int
 
@@ -1442,41 +1432,4 @@ class CacheResponse(BaseModel):
     user_reference: Optional[str] = None  # e.g., "my-app/npm-deps:lodash-4.17.21"
 
 
-class CacheResolveRequest(BaseModel):
-    """Request to cache an artifact by package coordinates (no URL required).
-
-    The server will construct the appropriate URL based on source_type and
-    configured upstream sources.
-    """
-    source_type: str
-    package: str
-    version: str
-    user_project: Optional[str] = None
-    user_package: Optional[str] = None
-    user_tag: Optional[str] = None
-
-    @field_validator('source_type')
-    @classmethod
-    def validate_source_type(cls, v: str) -> str:
-        if v not in SOURCE_TYPES:
-            raise ValueError(f"source_type must be one of: {', '.join(SOURCE_TYPES)}")
-        return v
-
-    @field_validator('package')
-    @classmethod
-    def validate_package(cls, v: str) -> str:
-        v = v.strip()
-        if not v:
-            raise ValueError("package cannot be empty")
-        return v
-
-    @field_validator('version')
-    @classmethod
-    def validate_version(cls, v: str) -> str:
-        v = v.strip()
-        if not v:
-            raise ValueError("version cannot be empty")
-        return v
-
-
 

backend/scripts/__init__.py

@@ -1 +0,0 @@
-# Scripts package

backend/scripts/backfill_pypi_dependencies.py

@@ -1,262 +0,0 @@
-#!/usr/bin/env python3
-"""
-Backfill script to extract dependencies from cached PyPI packages.
-
-This script scans all artifacts in the _pypi project and extracts
-Requires-Dist metadata from wheel and sdist files that don't already
-have dependencies recorded.
-
-Usage:
-    # From within the container:
-    python -m scripts.backfill_pypi_dependencies
-
-    # Or with docker exec:
-    docker exec orchard_orchard-server_1 python -m scripts.backfill_pypi_dependencies
-
-    # Dry run (preview only):
-    docker exec orchard_orchard-server_1 python -m scripts.backfill_pypi_dependencies --dry-run
-"""
-
-import argparse
-import logging
-import re
-import sys
-import tarfile
-import zipfile
-from io import BytesIO
-from typing import List, Optional, Tuple
-
-# Add parent directory to path for imports
-sys.path.insert(0, "/app")
-
-from sqlalchemy import create_engine
-from sqlalchemy.orm import sessionmaker
-
-from backend.app.config import get_settings
-from backend.app.models import (
-    Artifact,
-    ArtifactDependency,
-    Package,
-    Project,
-    Tag,
-)
-from backend.app.storage import get_storage
-
-logging.basicConfig(
-    level=logging.INFO,
-    format="%(asctime)s - %(levelname)s - %(message)s",
-)
-logger = logging.getLogger(__name__)
-
-
-def parse_requires_dist(requires_dist: str) -> Tuple[Optional[str], Optional[str]]:
-    """Parse a Requires-Dist line into (package_name, version_constraint)."""
-    # Remove any environment markers (after semicolon)
-    if ";" in requires_dist:
-        requires_dist = requires_dist.split(";")[0].strip()
-
-    # Match patterns like "package (>=1.0)" or "package>=1.0" or "package"
-    match = re.match(
-        r"^([a-zA-Z0-9][-a-zA-Z0-9._]*)\s*(?:\(([^)]+)\)|([<>=!~][^\s;]+))?",
-        requires_dist.strip(),
-    )
-
-    if not match:
-        return None, None
-
-    package_name = match.group(1)
-    version_constraint = match.group(2) or match.group(3)
-
-    # Normalize package name (PEP 503)
-    normalized_name = re.sub(r"[-_.]+", "-", package_name).lower()
-
-    if version_constraint:
-        version_constraint = version_constraint.strip()
-
-    return normalized_name, version_constraint
-
-
-def extract_requires_from_metadata(metadata_content: str) -> List[Tuple[str, Optional[str]]]:
-    """Extract all Requires-Dist entries from METADATA/PKG-INFO content."""
-    dependencies = []
-
-    for line in metadata_content.split("\n"):
-        if line.startswith("Requires-Dist:"):
-            value = line[len("Requires-Dist:"):].strip()
-            pkg_name, version = parse_requires_dist(value)
-            if pkg_name:
-                dependencies.append((pkg_name, version))
-
-    return dependencies
-
-
-def extract_metadata_from_wheel(content: bytes) -> Optional[str]:
-    """Extract METADATA file content from a wheel (zip) file."""
-    try:
-        with zipfile.ZipFile(BytesIO(content)) as zf:
-            for name in zf.namelist():
-                if name.endswith(".dist-info/METADATA"):
-                    return zf.read(name).decode("utf-8", errors="replace")
-    except Exception as e:
-        logger.warning(f"Failed to extract metadata from wheel: {e}")
-    return None
-
-
-def extract_metadata_from_sdist(content: bytes) -> Optional[str]:
-    """Extract PKG-INFO file content from a source distribution (.tar.gz)."""
-    try:
-        with tarfile.open(fileobj=BytesIO(content), mode="r:gz") as tf:
-            for member in tf.getmembers():
-                if member.name.endswith("/PKG-INFO") and member.name.count("/") == 1:
-                    f = tf.extractfile(member)
-                    if f:
-                        return f.read().decode("utf-8", errors="replace")
-    except Exception as e:
-        logger.warning(f"Failed to extract metadata from sdist: {e}")
-    return None
-
-
-def extract_dependencies(content: bytes, filename: str) -> List[Tuple[str, Optional[str]]]:
-    """Extract dependencies from a PyPI package file."""
-    metadata = None
-
-    if filename.endswith(".whl"):
-        metadata = extract_metadata_from_wheel(content)
-    elif filename.endswith(".tar.gz"):
-        metadata = extract_metadata_from_sdist(content)
-
-    if metadata:
-        return extract_requires_from_metadata(metadata)
-
-    return []
-
-
-def backfill_dependencies(dry_run: bool = False):
-    """Main backfill function."""
-    settings = get_settings()
-
-    # Create database connection
-    engine = create_engine(settings.database_url)
-    Session = sessionmaker(bind=engine)
-    db = Session()
-
-    # Create storage client
-    storage = get_storage()
-
-    try:
-        # Find the _pypi project
-        pypi_project = db.query(Project).filter(Project.name == "_pypi").first()
-        if not pypi_project:
-            logger.info("No _pypi project found. Nothing to backfill.")
-            return
-
-        # Get all packages in _pypi
-        packages = db.query(Package).filter(Package.project_id == pypi_project.id).all()
-        logger.info(f"Found {len(packages)} packages in _pypi project")
-
-        total_artifacts = 0
-        artifacts_with_deps = 0
-        artifacts_processed = 0
-        dependencies_added = 0
-
-        for package in packages:
-            # Get all tags (each tag points to an artifact)
-            tags = db.query(Tag).filter(Tag.package_id == package.id).all()
-
-            for tag in tags:
-                total_artifacts += 1
-                filename = tag.name
-
-                # Skip non-package files (like .metadata files)
-                if not (filename.endswith(".whl") or filename.endswith(".tar.gz")):
-                    continue
-
-                # Check if this artifact already has dependencies
-                existing_deps = db.query(ArtifactDependency).filter(
-                    ArtifactDependency.artifact_id == tag.artifact_id
-                ).count()
-
-                if existing_deps > 0:
-                    artifacts_with_deps += 1
-                    continue
-
-                # Get the artifact
-                artifact = db.query(Artifact).filter(Artifact.id == tag.artifact_id).first()
-                if not artifact:
-                    logger.warning(f"Artifact {tag.artifact_id} not found for tag {filename}")
-                    continue
-
-                logger.info(f"Processing {package.name}/{filename}...")
-
-                if dry_run:
-                    logger.info(f"  [DRY RUN] Would extract dependencies from {filename}")
-                    artifacts_processed += 1
-                    continue
-
-                # Download the artifact from S3
-                try:
-                    content = storage.get(artifact.s3_key)
-                except Exception as e:
-                    logger.error(f"  Failed to download {filename}: {e}")
-                    continue
-
-                # Extract dependencies
-                deps = extract_dependencies(content, filename)
-
-                if deps:
-                    logger.info(f"  Found {len(deps)} dependencies")
-                    for dep_name, dep_version in deps:
-                        # Check if already exists (race condition protection)
-                        existing = db.query(ArtifactDependency).filter(
-                            ArtifactDependency.artifact_id == tag.artifact_id,
-                            ArtifactDependency.dependency_project == "_pypi",
-                            ArtifactDependency.dependency_package == dep_name,
-                        ).first()
-
-                        if not existing:
-                            dep = ArtifactDependency(
-                                artifact_id=tag.artifact_id,
-                                dependency_project="_pypi",
-                                dependency_package=dep_name,
-                                version_constraint=dep_version if dep_version else "*",
-                            )
-                            db.add(dep)
-                            dependencies_added += 1
-                            logger.info(f"    + {dep_name} {dep_version or '*'}")
-
-                    db.commit()
-                else:
-                    logger.info(f"  No dependencies found")
-
-                artifacts_processed += 1
-
-        logger.info("")
-        logger.info("=" * 50)
-        logger.info("Backfill complete!")
-        logger.info(f"  Total artifacts: {total_artifacts}")
-        logger.info(f"  Already had deps: {artifacts_with_deps}")
-        logger.info(f"  Processed: {artifacts_processed}")
-        logger.info(f"  Dependencies added: {dependencies_added}")
-        if dry_run:
-            logger.info("  (DRY RUN - no changes made)")
-
-    finally:
-        db.close()
-
-
-def main():
-    parser = argparse.ArgumentParser(
-        description="Backfill dependencies for cached PyPI packages"
-    )
-    parser.add_argument(
-        "--dry-run",
-        action="store_true",
-        help="Preview what would be done without making changes",
-    )
-    args = parser.parse_args()
-
-    backfill_dependencies(dry_run=args.dry_run)
-
-
-if __name__ == "__main__":
-    main()

backend/tests/integration/test_projects_api.py

@@ -128,9 +128,7 @@ class TestProjectListingFilters:
         assert response.status_code == 200
 
         data = response.json()
-        # Filter out system projects (names starting with "_") as they may have
-        # collation-specific sort behavior and aren't part of the test data
-        names = [p["name"] for p in data["items"] if not p["name"].startswith("_")]
+        names = [p["name"] for p in data["items"]]
         assert names == sorted(names)
 
 

backend/tests/integration/test_pypi_proxy.py

@@ -1,137 +0,0 @@
-"""Integration tests for PyPI transparent proxy."""
-
-import os
-import pytest
-import httpx
-
-
-def get_base_url():
-    """Get the base URL for the Orchard server from environment."""
-    return os.environ.get("ORCHARD_TEST_URL", "http://localhost:8080")
-
-
-class TestPyPIProxyEndpoints:
-    """Tests for PyPI proxy endpoints.
-
-    These endpoints are public (no auth required) since pip needs to use them.
-    """
-
-    @pytest.mark.integration
-    def test_pypi_simple_index(self):
-        """Test that /pypi/simple/ returns HTML response."""
-        with httpx.Client(base_url=get_base_url(), timeout=30.0) as client:
-            response = client.get("/pypi/simple/")
-            # Returns 200 if sources configured, 503 if not
-            assert response.status_code in (200, 503)
-            if response.status_code == 200:
-                assert "text/html" in response.headers.get("content-type", "")
-            else:
-                assert "No PyPI upstream sources configured" in response.json()["detail"]
-
-    @pytest.mark.integration
-    def test_pypi_package_endpoint(self):
-        """Test that /pypi/simple/{package}/ returns appropriate response."""
-        with httpx.Client(base_url=get_base_url(), timeout=30.0) as client:
-            response = client.get("/pypi/simple/requests/")
-            # Returns 200 if sources configured and package found,
-            # 404 if package not found, 503 if no sources
-            assert response.status_code in (200, 404, 503)
-            if response.status_code == 200:
-                assert "text/html" in response.headers.get("content-type", "")
-            elif response.status_code == 404:
-                assert "not found" in response.json()["detail"].lower()
-            else:  # 503
-                assert "No PyPI upstream sources configured" in response.json()["detail"]
-
-    @pytest.mark.integration
-    def test_pypi_download_missing_upstream_param(self):
-        """Test that /pypi/simple/{package}/{filename} requires upstream param."""
-        with httpx.Client(base_url=get_base_url(), timeout=30.0) as client:
-            response = client.get("/pypi/simple/requests/requests-2.31.0.tar.gz")
-            assert response.status_code == 400
-            assert "upstream" in response.json()["detail"].lower()
-
-
-class TestPyPILinkRewriting:
-    """Tests for URL rewriting in PyPI proxy responses."""
-
-    def test_rewrite_package_links(self):
-        """Test that download links are rewritten to go through proxy."""
-        from app.pypi_proxy import _rewrite_package_links
-
-        html = '''
-        <html>
-        <body>
-        <a href="https://files.pythonhosted.org/packages/ab/cd/requests-2.31.0.tar.gz#sha256=abc123">requests-2.31.0.tar.gz</a>
-        <a href="https://files.pythonhosted.org/packages/ef/gh/requests-2.31.0-py3-none-any.whl#sha256=def456">requests-2.31.0-py3-none-any.whl</a>
-        </body>
-        </html>
-        '''
-
-        # upstream_base_url is used to resolve relative URLs (not needed here since URLs are absolute)
-        result = _rewrite_package_links(
-            html,
-            "http://localhost:8080",
-            "requests",
-            "https://pypi.org/simple/requests/"
-        )
-
-        # Links should be rewritten to go through our proxy
-        assert "/pypi/simple/requests/requests-2.31.0.tar.gz?upstream=" in result
-        assert "/pypi/simple/requests/requests-2.31.0-py3-none-any.whl?upstream=" in result
-        # Original URLs should be encoded in upstream param
-        assert "files.pythonhosted.org" in result
-        # Hash fragments should be preserved
-        assert "#sha256=abc123" in result
-        assert "#sha256=def456" in result
-
-    def test_rewrite_relative_links(self):
-        """Test that relative URLs are resolved to absolute URLs."""
-        from app.pypi_proxy import _rewrite_package_links
-
-        # Artifactory-style relative URLs
-        html = '''
-        <html>
-        <body>
-        <a href="../../packages/ab/cd/requests-2.31.0.tar.gz#sha256=abc123">requests-2.31.0.tar.gz</a>
-        </body>
-        </html>
-        '''
-
-        result = _rewrite_package_links(
-            html,
-            "https://orchard.example.com",
-            "requests",
-            "https://artifactory.example.com/api/pypi/pypi-remote/simple/requests/"
-        )
-
-        # The relative URL should be resolved to absolute
-        # ../../packages/ab/cd/... from /api/pypi/pypi-remote/simple/requests/ resolves to /api/pypi/pypi-remote/packages/ab/cd/...
-        assert "upstream=https%3A%2F%2Fartifactory.example.com%2Fapi%2Fpypi%2Fpypi-remote%2Fpackages" in result
-        # Hash fragment should be preserved
-        assert "#sha256=abc123" in result
-
-
-class TestPyPIPackageNormalization:
-    """Tests for PyPI package name normalization."""
-
-    @pytest.mark.integration
-    def test_package_name_normalized(self):
-        """Test that package names are normalized per PEP 503.
-
-        Different capitalizations/separators should all be valid paths.
-        The endpoint normalizes to lowercase with hyphens before lookup.
-        """
-        with httpx.Client(base_url=get_base_url(), timeout=30.0) as client:
-            # Test various name formats - all should be valid endpoint paths
-            for package_name in ["Requests", "some_package", "some-package"]:
-                response = client.get(f"/pypi/simple/{package_name}/")
-                # 200 = found, 404 = not found, 503 = no sources configured
-                assert response.status_code in (200, 404, 503), \
-                    f"Unexpected status {response.status_code} for {package_name}"
-
-                # Verify response is appropriate for the status code
-                if response.status_code == 200:
-                    assert "text/html" in response.headers.get("content-type", "")
-                elif response.status_code == 503:
-                    assert "No PyPI upstream sources configured" in response.json()["detail"]

frontend/package-lock.json

@@ -8,12 +8,9 @@
       "name": "orchard-frontend",
       "version": "1.0.0",
       "dependencies": {
-        "@types/dagre": "^0.7.53",
-        "dagre": "^0.8.5",
         "react": "^18.2.0",
         "react-dom": "^18.2.0",
-        "react-router-dom": "6.28.0",
-        "reactflow": "^11.11.4"
+        "react-router-dom": "6.28.0"
       },
       "devDependencies": {
         "@testing-library/jest-dom": "^6.4.2",
@@ -946,102 +943,6 @@
         "@jridgewell/sourcemap-codec": "^1.4.14"
       }
     },
-    "node_modules/@reactflow/background": {
-      "version": "11.3.14",
-      "resolved": "https://registry.npmjs.org/@reactflow/background/-/background-11.3.14.tgz",
-      "integrity": "sha512-Gewd7blEVT5Lh6jqrvOgd4G6Qk17eGKQfsDXgyRSqM+CTwDqRldG2LsWN4sNeno6sbqVIC2fZ+rAUBFA9ZEUDA==",
-      "dependencies": {
-        "@reactflow/core": "11.11.4",
-        "classcat": "^5.0.3",
-        "zustand": "^4.4.1"
-      },
-      "peerDependencies": {
-        "react": ">=17",
-        "react-dom": ">=17"
-      }
-    },
-    "node_modules/@reactflow/controls": {
-      "version": "11.2.14",
-      "resolved": "https://registry.npmjs.org/@reactflow/controls/-/controls-11.2.14.tgz",
-      "integrity": "sha512-MiJp5VldFD7FrqaBNIrQ85dxChrG6ivuZ+dcFhPQUwOK3HfYgX2RHdBua+gx+40p5Vw5It3dVNp/my4Z3jF0dw==",
-      "dependencies": {
-        "@reactflow/core": "11.11.4",
-        "classcat": "^5.0.3",
-        "zustand": "^4.4.1"
-      },
-      "peerDependencies": {
-        "react": ">=17",
-        "react-dom": ">=17"
-      }
-    },
-    "node_modules/@reactflow/core": {
-      "version": "11.11.4",
-      "resolved": "https://registry.npmjs.org/@reactflow/core/-/core-11.11.4.tgz",
-      "integrity": "sha512-H4vODklsjAq3AMq6Np4LE12i1I4Ta9PrDHuBR9GmL8uzTt2l2jh4CiQbEMpvMDcp7xi4be0hgXj+Ysodde/i7Q==",
-      "dependencies": {
-        "@types/d3": "^7.4.0",
-        "@types/d3-drag": "^3.0.1",
-        "@types/d3-selection": "^3.0.3",
-        "@types/d3-zoom": "^3.0.1",
-        "classcat": "^5.0.3",
-        "d3-drag": "^3.0.0",
-        "d3-selection": "^3.0.0",
-        "d3-zoom": "^3.0.0",
-        "zustand": "^4.4.1"
-      },
-      "peerDependencies": {
-        "react": ">=17",
-        "react-dom": ">=17"
-      }
-    },
-    "node_modules/@reactflow/minimap": {
-      "version": "11.7.14",
-      "resolved": "https://registry.npmjs.org/@reactflow/minimap/-/minimap-11.7.14.tgz",
-      "integrity": "sha512-mpwLKKrEAofgFJdkhwR5UQ1JYWlcAAL/ZU/bctBkuNTT1yqV+y0buoNVImsRehVYhJwffSWeSHaBR5/GJjlCSQ==",
-      "dependencies": {
-        "@reactflow/core": "11.11.4",
-        "@types/d3-selection": "^3.0.3",
-        "@types/d3-zoom": "^3.0.1",
-        "classcat": "^5.0.3",
-        "d3-selection": "^3.0.0",
-        "d3-zoom": "^3.0.0",
-        "zustand": "^4.4.1"
-      },
-      "peerDependencies": {
-        "react": ">=17",
-        "react-dom": ">=17"
-      }
-    },
-    "node_modules/@reactflow/node-resizer": {
-      "version": "2.2.14",
-      "resolved": "https://registry.npmjs.org/@reactflow/node-resizer/-/node-resizer-2.2.14.tgz",
-      "integrity": "sha512-fwqnks83jUlYr6OHcdFEedumWKChTHRGw/kbCxj0oqBd+ekfs+SIp4ddyNU0pdx96JIm5iNFS0oNrmEiJbbSaA==",
-      "dependencies": {
-        "@reactflow/core": "11.11.4",
-        "classcat": "^5.0.4",
-        "d3-drag": "^3.0.0",
-        "d3-selection": "^3.0.0",
-        "zustand": "^4.4.1"
-      },
-      "peerDependencies": {
-        "react": ">=17",
-        "react-dom": ">=17"
-      }
-    },
-    "node_modules/@reactflow/node-toolbar": {
-      "version": "1.3.14",
-      "resolved": "https://registry.npmjs.org/@reactflow/node-toolbar/-/node-toolbar-1.3.14.tgz",
-      "integrity": "sha512-rbynXQnH/xFNu4P9H+hVqlEUafDCkEoCy0Dg9mG22Sg+rY/0ck6KkrAQrYrTgXusd+cEJOMK0uOOFCK2/5rSGQ==",
-      "dependencies": {
-        "@reactflow/core": "11.11.4",
-        "classcat": "^5.0.3",
-        "zustand": "^4.4.1"
-      },
-      "peerDependencies": {
-        "react": ">=17",
-        "react-dom": ">=17"
-      }
-    },
     "node_modules/@remix-run/router": {
       "version": "1.21.0",
       "resolved": "https://registry.npmjs.org/@remix-run/router/-/router-1.21.0.tgz",
@@ -1536,233 +1437,6 @@
         "@babel/types": "^7.28.2"
       }
     },
-    "node_modules/@types/d3": {
-      "version": "7.4.3",
-      "resolved": "https://registry.npmjs.org/@types/d3/-/d3-7.4.3.tgz",
-      "integrity": "sha512-lZXZ9ckh5R8uiFVt8ogUNf+pIrK4EsWrx2Np75WvF/eTpJ0FMHNhjXk8CKEx/+gpHbNQyJWehbFaTvqmHWB3ww==",
-      "dependencies": {
-        "@types/d3-array": "*",
-        "@types/d3-axis": "*",
-        "@types/d3-brush": "*",
-        "@types/d3-chord": "*",
-        "@types/d3-color": "*",
-        "@types/d3-contour": "*",
-        "@types/d3-delaunay": "*",
-        "@types/d3-dispatch": "*",
-        "@types/d3-drag": "*",
-        "@types/d3-dsv": "*",
-        "@types/d3-ease": "*",
-        "@types/d3-fetch": "*",
-        "@types/d3-force": "*",
-        "@types/d3-format": "*",
-        "@types/d3-geo": "*",
-        "@types/d3-hierarchy": "*",
-        "@types/d3-interpolate": "*",
-        "@types/d3-path": "*",
-        "@types/d3-polygon": "*",
-        "@types/d3-quadtree": "*",
-        "@types/d3-random": "*",
-        "@types/d3-scale": "*",
-        "@types/d3-scale-chromatic": "*",
-        "@types/d3-selection": "*",
-        "@types/d3-shape": "*",
-        "@types/d3-time": "*",
-        "@types/d3-time-format": "*",
-        "@types/d3-timer": "*",
-        "@types/d3-transition": "*",
-        "@types/d3-zoom": "*"
-      }
-    },
-    "node_modules/@types/d3-array": {
-      "version": "3.2.2",
-      "resolved": "https://registry.npmjs.org/@types/d3-array/-/d3-array-3.2.2.tgz",
-      "integrity": "sha512-hOLWVbm7uRza0BYXpIIW5pxfrKe0W+D5lrFiAEYR+pb6w3N2SwSMaJbXdUfSEv+dT4MfHBLtn5js0LAWaO6otw=="
-    },
-    "node_modules/@types/d3-axis": {
-      "version": "3.0.6",
-      "resolved": "https://registry.npmjs.org/@types/d3-axis/-/d3-axis-3.0.6.tgz",
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       "version": "1.1.0",
       "resolved": "https://registry.npmjs.org/has-bigints/-/has-bigints-1.1.0.tgz",
@@ -3646,11 +3197,6 @@
         "url": "https://github.com/sponsors/antfu"
       }
     },
-    "node_modules/lodash": {
-      "version": "4.17.23",
-      "resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.23.tgz",
-      "integrity": "sha512-LgVTMpQtIopCi79SJeDiP0TfWi5CNEc/L/aRdTh3yIvmZXTnheWpKjSZhnvMl8iXbC1tFg9gdHHDMLoV7CnG+w=="
-    },
     "node_modules/loose-envify": {
       "version": "1.4.0",
       "resolved": "https://registry.npmjs.org/loose-envify/-/loose-envify-1.4.0.tgz",
@@ -4240,23 +3786,6 @@
         "react-dom": ">=16.8"
       }
     },
-    "node_modules/reactflow": {
-      "version": "11.11.4",
-      "resolved": "https://registry.npmjs.org/reactflow/-/reactflow-11.11.4.tgz",
-      "integrity": "sha512-70FOtJkUWH3BAOsN+LU9lCrKoKbtOPnz2uq0CV2PLdNSwxTXOhCbsZr50GmZ+Rtw3jx8Uv7/vBFtCGixLfd4Og==",
-      "dependencies": {
-        "@reactflow/background": "11.3.14",
-        "@reactflow/controls": "11.2.14",
-        "@reactflow/core": "11.11.4",
-        "@reactflow/minimap": "11.7.14",
-        "@reactflow/node-resizer": "2.2.14",
-        "@reactflow/node-toolbar": "1.3.14"
-      },
-      "peerDependencies": {
-        "react": ">=17",
-        "react-dom": ">=17"
-      }
-    },
     "node_modules/redent": {
       "version": "3.0.0",
       "resolved": "https://registry.npmjs.org/redent/-/redent-3.0.0.tgz",
@@ -4815,14 +4344,6 @@
         "requires-port": "^1.0.0"
       }
     },
-    "node_modules/use-sync-external-store": {
-      "version": "1.6.0",
-      "resolved": "https://registry.npmjs.org/use-sync-external-store/-/use-sync-external-store-1.6.0.tgz",
-      "integrity": "sha512-Pp6GSwGP/NrPIrxVFAIkOQeyw8lFenOHijQWkUTrDvrF4ALqylP2C/KCkeS9dpUM3KvYRQhna5vt7IL95+ZQ9w==",
-      "peerDependencies": {
-        "react": "^16.8.0 || ^17.0.0 || ^18.0.0 || ^19.0.0"
-      }
-    },
     "node_modules/vite": {
       "version": "5.4.21",
       "resolved": "https://registry.npmjs.org/vite/-/vite-5.4.21.tgz",
@@ -5191,33 +4712,6 @@
       "funding": {
         "url": "https://github.com/sponsors/sindresorhus"
       }
-    },
-    "node_modules/zustand": {
-      "version": "4.5.7",
-      "resolved": "https://registry.npmjs.org/zustand/-/zustand-4.5.7.tgz",
-      "integrity": "sha512-CHOUy7mu3lbD6o6LJLfllpjkzhHXSBlX8B9+qPddUsIfeF5S/UZ5q0kmCsnRqT1UHFQZchNFDDzMbQsuesHWlw==",
-      "dependencies": {
-        "use-sync-external-store": "^1.2.2"
-      },
-      "engines": {
-        "node": ">=12.7.0"
-      },
-      "peerDependencies": {
-        "@types/react": ">=16.8",
-        "immer": ">=9.0.6",
-        "react": ">=16.8"
-      },
-      "peerDependenciesMeta": {
-        "@types/react": {
-          "optional": true
-        },
-        "immer": {
-          "optional": true
-        },
-        "react": {
-          "optional": true
-        }
-      }
     }
   }
 }

frontend/package.json

@@ -12,12 +12,9 @@
     "test:coverage": "vitest run --coverage"
   },
   "dependencies": {
-    "@types/dagre": "^0.7.53",
-    "dagre": "^0.8.5",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",
-    "react-router-dom": "6.28.0",
-    "reactflow": "^11.11.4"
+    "react-router-dom": "6.28.0"
   },
   "devDependencies": {
     "@testing-library/jest-dom": "^6.4.2",

frontend/src/api.ts

@@ -46,6 +46,8 @@ import {
   UpstreamSourceCreate,
   UpstreamSourceUpdate,
   UpstreamSourceTestResult,
+  CacheSettings,
+  CacheSettingsUpdate,
 } from './types';
 
 const API_BASE = '/api/v1';
@@ -78,13 +80,7 @@ export class ForbiddenError extends ApiError {
 async function handleResponse<T>(response: Response): Promise<T> {
   if (!response.ok) {
     const error = await response.json().catch(() => ({ detail: 'Unknown error' }));
-    // Handle detail as string or object (backend may return structured errors)
-    let message: string;
-    if (typeof error.detail === 'object') {
-      message = JSON.stringify(error.detail);
-    } else {
-      message = error.detail || `HTTP ${response.status}`;
-    }
+    const message = error.detail || `HTTP ${response.status}`;
 
     if (response.status === 401) {
       throw new UnauthorizedError(message);
@@ -753,3 +749,20 @@ export async function testUpstreamSource(id: string): Promise<UpstreamSourceTest
   return handleResponse<UpstreamSourceTestResult>(response);
 }
 
+// Cache Settings Admin API
+export async function getCacheSettings(): Promise<CacheSettings> {
+  const response = await fetch(`${API_BASE}/admin/cache-settings`, {
+    credentials: 'include',
+  });
+  return handleResponse<CacheSettings>(response);
+}
+
+export async function updateCacheSettings(data: CacheSettingsUpdate): Promise<CacheSettings> {
+  const response = await fetch(`${API_BASE}/admin/cache-settings`, {
+    method: 'PUT',
+    headers: { 'Content-Type': 'application/json' },
+    body: JSON.stringify(data),
+    credentials: 'include',
+  });
+  return handleResponse<CacheSettings>(response);
+}

frontend/src/components/DependencyGraph.css

@@ -55,10 +55,6 @@
   font-size: 0.8125rem;
 }
 
-.missing-count {
-  color: #f59e0b;
-}
-
 .close-btn {
   background: transparent;
   border: none;
@@ -76,115 +72,171 @@
   color: var(--text-primary);
 }
 
+.dependency-graph-toolbar {
+  display: flex;
+  align-items: center;
+  gap: 8px;
+  padding: 12px 20px;
+  border-bottom: 1px solid var(--border-primary);
+  background: var(--bg-secondary);
+}
+
+.zoom-level {
+  margin-left: auto;
+  font-size: 0.8125rem;
+  color: var(--text-muted);
+  font-family: 'JetBrains Mono', monospace;
+}
+
 .dependency-graph-container {
   flex: 1;
   overflow: hidden;
   position: relative;
-  background: var(--bg-primary);
+  background:
+    linear-gradient(90deg, var(--border-primary) 1px, transparent 1px),
+    linear-gradient(var(--border-primary) 1px, transparent 1px);
+  background-size: 20px 20px;
+  background-position: center center;
 }
 
-/* React Flow Customization */
-.react-flow__background {
-  background-color: var(--bg-primary) !important;
+.graph-canvas {
+  padding: 40px;
+  min-width: 100%;
+  min-height: 100%;
+  transform-origin: center center;
+  transition: transform 0.1s ease-out;
 }
 
-.react-flow__controls {
-  background: var(--bg-tertiary);
-  border: 1px solid var(--border-primary);
-  border-radius: var(--radius-md);
-  box-shadow: 0 4px 12px rgba(0, 0, 0, 0.3);
+/* Graph Nodes */
+.graph-node-container {
+  display: flex;
+  flex-direction: column;
+  align-items: flex-start;
 }
 
-.react-flow__controls-button {
-  background: var(--bg-tertiary);
-  border: none;
-  border-bottom: 1px solid var(--border-primary);
-  color: var(--text-secondary);
-  width: 28px;
-  height: 28px;
-}
-
-.react-flow__controls-button:hover {
-  background: var(--bg-hover);
-  color: var(--text-primary);
-}
-
-.react-flow__controls-button:last-child {
-  border-bottom: none;
-}
-
-.react-flow__controls-button svg {
-  fill: currentColor;
-}
-
-.react-flow__attribution {
-  background: transparent !important;
-}
-
-.react-flow__attribution a {
-  color: var(--text-muted) !important;
-  font-size: 10px;
-}
-
-/* Custom Flow Nodes */
-.flow-node {
+.graph-node {
   background: var(--bg-tertiary);
   border: 2px solid var(--border-primary);
   border-radius: var(--radius-md);
   padding: 12px 16px;
-  min-width: 160px;
+  min-width: 200px;
   cursor: pointer;
   transition: all var(--transition-fast);
-  text-align: center;
+  position: relative;
 }
 
-.flow-node:hover {
+.graph-node:hover {
   border-color: var(--accent-primary);
   box-shadow: 0 4px 12px rgba(16, 185, 129, 0.2);
 }
 
-.flow-node--root {
+.graph-node--root {
   background: linear-gradient(135deg, rgba(16, 185, 129, 0.15) 0%, rgba(5, 150, 105, 0.15) 100%);
   border-color: var(--accent-primary);
 }
 
-.flow-node__name {
+.graph-node--hovered {
+  transform: scale(1.02);
+}
+
+.graph-node__header {
+  display: flex;
+  align-items: center;
+  gap: 8px;
+  margin-bottom: 4px;
+}
+
+.graph-node__name {
   font-weight: 600;
   color: var(--accent-primary);
   font-family: 'JetBrains Mono', monospace;
-  font-size: 0.8125rem;
-  margin-bottom: 4px;
-  word-break: break-word;
+  font-size: 0.875rem;
 }
 
-.flow-node__details {
+.graph-node__toggle {
+  background: var(--bg-hover);
+  border: 1px solid var(--border-primary);
+  border-radius: 4px;
+  width: 20px;
+  height: 20px;
   display: flex;
   align-items: center;
   justify-content: center;
-  gap: 8px;
-  font-size: 0.6875rem;
+  cursor: pointer;
+  font-size: 0.875rem;
+  color: var(--text-secondary);
+  font-weight: 600;
+  margin-left: auto;
+}
+
+.graph-node__toggle:hover {
+  background: var(--bg-tertiary);
+  color: var(--text-primary);
+}
+
+.graph-node__details {
+  display: flex;
+  align-items: center;
+  gap: 12px;
+  font-size: 0.75rem;
   color: var(--text-muted);
 }
 
-.flow-node__version {
+.graph-node__version {
   font-family: 'JetBrains Mono', monospace;
   color: var(--text-secondary);
 }
 
-.flow-node__size {
+.graph-node__size {
   color: var(--text-muted);
 }
 
-/* Flow Handles (connection points) */
-.flow-handle {
-  width: 8px !important;
-  height: 8px !important;
-  background: var(--border-primary) !important;
-  border: 2px solid var(--bg-tertiary) !important;
+/* Graph Children / Tree Structure */
+.graph-children {
+  display: flex;
+  padding-left: 24px;
+  margin-top: 8px;
+  position: relative;
 }
 
-.flow-node:hover .flow-handle {
-  background: var(--accent-primary) !important;
+.graph-connector {
+  position: absolute;
+  left: 12px;
+  top: 0;
+  bottom: 50%;
+  width: 12px;
+  border-left: 2px solid var(--border-primary);
+  border-bottom: 2px solid var(--border-primary);
+  border-bottom-left-radius: 8px;
+}
+
+.graph-children-list {
+  display: flex;
+  flex-direction: column;
+  gap: 8px;
+  position: relative;
+}
+
+.graph-children-list::before {
+  content: '';
+  position: absolute;
+  left: -12px;
+  top: 20px;
+  bottom: 20px;
+  border-left: 2px solid var(--border-primary);
+}
+
+.graph-children-list > .graph-node-container {
+  position: relative;
+}
+
+.graph-children-list > .graph-node-container::before {
+  content: '';
+  position: absolute;
+  left: -12px;
+  top: 20px;
+  width: 12px;
+  border-top: 2px solid var(--border-primary);
 }
 
 /* Loading, Error, Empty States */
@@ -227,61 +279,39 @@
   line-height: 1.5;
 }
 
-/* Missing Dependencies */
-.missing-dependencies {
-  border-top: 1px solid var(--border-primary);
-  padding: 16px 20px;
-  background: rgba(245, 158, 11, 0.05);
-  max-height: 200px;
-  overflow-y: auto;
-}
-
-.missing-dependencies h3 {
-  margin: 0 0 8px 0;
-  font-size: 0.875rem;
-  font-weight: 600;
-  color: #f59e0b;
-}
-
-.missing-hint {
-  margin: 0 0 12px 0;
-  font-size: 0.75rem;
-  color: var(--text-muted);
-}
-
-.missing-list {
-  list-style: none;
-  padding: 0;
-  margin: 0;
-  display: flex;
-  flex-wrap: wrap;
-  gap: 8px;
-}
-
-.missing-item {
-  display: inline-flex;
-  align-items: center;
-  gap: 4px;
+/* Tooltip */
+.graph-tooltip {
+  position: fixed;
+  bottom: 24px;
+  left: 50%;
+  transform: translateX(-50%);
   background: var(--bg-tertiary);
-  border: 1px solid rgba(245, 158, 11, 0.3);
-  border-radius: var(--radius-sm);
-  padding: 4px 8px;
-  font-size: 0.75rem;
+  border: 1px solid var(--border-primary);
+  border-radius: var(--radius-md);
+  padding: 12px 16px;
+  font-size: 0.8125rem;
+  box-shadow: 0 8px 24px rgba(0, 0, 0, 0.4);
+  z-index: 1001;
 }
 
-.missing-name {
+.graph-tooltip strong {
+  display: block;
+  color: var(--accent-primary);
   font-family: 'JetBrains Mono', monospace;
+  margin-bottom: 4px;
+}
+
+.graph-tooltip div {
   color: var(--text-secondary);
+  margin-top: 2px;
 }
 
-.missing-constraint {
+.tooltip-hint {
+  margin-top: 8px;
+  padding-top: 8px;
+  border-top: 1px solid var(--border-primary);
   color: var(--text-muted);
-  font-family: 'JetBrains Mono', monospace;
-}
-
-.missing-required-by {
-  color: var(--text-muted);
-  font-size: 0.6875rem;
+  font-size: 0.75rem;
 }
 
 /* Responsive */

frontend/src/components/DependencyGraph.tsx

@@ -1,19 +1,5 @@
-import { useState, useEffect, useCallback, useMemo } from 'react';
+import { useState, useEffect, useCallback, useRef } from 'react';
 import { useNavigate } from 'react-router-dom';
-import ReactFlow, {
-  Node,
-  Edge,
-  Controls,
-  Background,
-  useNodesState,
-  useEdgesState,
-  MarkerType,
-  NodeProps,
-  Handle,
-  Position,
-} from 'reactflow';
-import dagre from 'dagre';
-import 'reactflow/dist/style.css';
 import { ResolvedArtifact, DependencyResolutionResponse, Dependency } from '../types';
 import { resolveDependencies, getArtifactDependencies } from '../api';
 import './DependencyGraph.css';
@@ -25,14 +11,15 @@ interface DependencyGraphProps {
   onClose: () => void;
 }
 
-interface NodeData {
-  label: string;
+interface GraphNode {
+  id: string;
   project: string;
   package: string;
   version: string | null;
   size: number;
-  isRoot: boolean;
-  onNavigate: (project: string, pkg: string) => void;
+  depth: number;
+  children: GraphNode[];
+  isRoot?: boolean;
 }
 
 function formatBytes(bytes: number): string {
@@ -43,89 +30,29 @@ function formatBytes(bytes: number): string {
   return parseFloat((bytes / Math.pow(k, i)).toFixed(1)) + ' ' + sizes[i];
 }
 
-// Custom node component
-function DependencyNode({ data }: NodeProps<NodeData>) {
-  return (
-    <div
-      className={`flow-node ${data.isRoot ? 'flow-node--root' : ''}`}
-      onClick={() => data.onNavigate(data.project, data.package)}
-    >
-      <Handle type="target" position={Position.Top} className="flow-handle" />
-      <div className="flow-node__name">{data.package}</div>
-      <div className="flow-node__details">
-        {data.version && <span className="flow-node__version">{data.version}</span>}
-        <span className="flow-node__size">{formatBytes(data.size)}</span>
-      </div>
-      <Handle type="source" position={Position.Bottom} className="flow-handle" />
-    </div>
-  );
-}
-
-const nodeTypes = { dependency: DependencyNode };
-
-// Dagre layout function
-function getLayoutedElements(
-  nodes: Node<NodeData>[],
-  edges: Edge[],
-  direction: 'TB' | 'LR' = 'TB'
-) {
-  const dagreGraph = new dagre.graphlib.Graph();
-  dagreGraph.setDefaultEdgeLabel(() => ({}));
-
-  const nodeWidth = 180;
-  const nodeHeight = 60;
-
-  dagreGraph.setGraph({ rankdir: direction, nodesep: 50, ranksep: 80 });
-
-  nodes.forEach((node) => {
-    dagreGraph.setNode(node.id, { width: nodeWidth, height: nodeHeight });
-  });
-
-  edges.forEach((edge) => {
-    dagreGraph.setEdge(edge.source, edge.target);
-  });
-
-  dagre.layout(dagreGraph);
-
-  const layoutedNodes = nodes.map((node) => {
-    const nodeWithPosition = dagreGraph.node(node.id);
-    return {
-      ...node,
-      position: {
-        x: nodeWithPosition.x - nodeWidth / 2,
-        y: nodeWithPosition.y - nodeHeight / 2,
-      },
-    };
-  });
-
-  return { nodes: layoutedNodes, edges };
-}
-
 function DependencyGraph({ projectName, packageName, tagName, onClose }: DependencyGraphProps) {
   const navigate = useNavigate();
+  const containerRef = useRef<HTMLDivElement>(null);
 
   const [loading, setLoading] = useState(true);
   const [error, setError] = useState<string | null>(null);
   const [resolution, setResolution] = useState<DependencyResolutionResponse | null>(null);
-  const [nodes, setNodes, onNodesChange] = useNodesState<NodeData>([]);
-  const [edges, setEdges, onEdgesChange] = useEdgesState([]);
-
-  const handleNavigate = useCallback((project: string, pkg: string) => {
-    navigate(`/project/${project}/${pkg}`);
-    onClose();
-  }, [navigate, onClose]);
+  const [graphRoot, setGraphRoot] = useState<GraphNode | null>(null);
+  const [hoveredNode, setHoveredNode] = useState<GraphNode | null>(null);
+  const [zoom, setZoom] = useState(1);
+  const [pan, setPan] = useState({ x: 0, y: 0 });
+  const [isDragging, setIsDragging] = useState(false);
+  const [dragStart, setDragStart] = useState({ x: 0, y: 0 });
+  const [collapsedNodes, setCollapsedNodes] = useState<Set<string>>(new Set());
 
   // Build graph structure from resolution data
-  const buildFlowGraph = useCallback(async (
-    resolutionData: DependencyResolutionResponse,
-    onNavigate: (project: string, pkg: string) => void
-  ) => {
+  const buildGraph = useCallback(async (resolutionData: DependencyResolutionResponse) => {
     const artifactMap = new Map<string, ResolvedArtifact>();
     resolutionData.resolved.forEach(artifact => {
       artifactMap.set(artifact.artifact_id, artifact);
     });
 
-    // Fetch dependencies for each artifact
+    // Fetch dependencies for each artifact to build the tree
     const depsMap = new Map<string, Dependency[]>();
 
     for (const artifact of resolutionData.resolved) {
@@ -137,82 +64,50 @@ function DependencyGraph({ projectName, packageName, tagName, onClose }: Depende
       }
     }
 
-    // Find the root artifact
+    // Find the root artifact (the requested one)
     const rootArtifact = resolutionData.resolved.find(
       a => a.project === resolutionData.requested.project &&
            a.package === resolutionData.requested.package
     );
 
     if (!rootArtifact) {
-      return { nodes: [], edges: [] };
+      return null;
     }
 
-    const flowNodes: Node<NodeData>[] = [];
-    const flowEdges: Edge[] = [];
+    // Build tree recursively
     const visited = new Set<string>();
-    const nodeIdMap = new Map<string, string>(); // artifact_id -> node id
-
-    // Build nodes and edges recursively
-    const processNode = (artifact: ResolvedArtifact, isRoot: boolean) => {
-      if (visited.has(artifact.artifact_id)) {
-        return nodeIdMap.get(artifact.artifact_id);
-      }
 
+    const buildNode = (artifact: ResolvedArtifact, depth: number): GraphNode => {
+      const nodeId = `${artifact.project}/${artifact.package}`;
       visited.add(artifact.artifact_id);
-      const nodeId = `node-${flowNodes.length}`;
-      nodeIdMap.set(artifact.artifact_id, nodeId);
-
-      flowNodes.push({
-        id: nodeId,
-        type: 'dependency',
-        position: { x: 0, y: 0 }, // Will be set by dagre
-        data: {
-          label: `${artifact.project}/${artifact.package}`,
-          project: artifact.project,
-          package: artifact.package,
-          version: artifact.version || artifact.tag,
-          size: artifact.size,
-          isRoot,
-          onNavigate,
-        },
-      });
 
       const deps = depsMap.get(artifact.artifact_id) || [];
+      const children: GraphNode[] = [];
 
       for (const dep of deps) {
+        // Find the resolved artifact for this dependency
         const childArtifact = resolutionData.resolved.find(
           a => a.project === dep.project && a.package === dep.package
         );
 
-        if (childArtifact) {
-          const childNodeId = processNode(childArtifact, false);
-          if (childNodeId) {
-            flowEdges.push({
-              id: `edge-${nodeId}-${childNodeId}`,
-              source: nodeId,
-              target: childNodeId,
-              markerEnd: {
-                type: MarkerType.ArrowClosed,
-                width: 15,
-                height: 15,
-                color: 'var(--accent-primary)',
-              },
-              style: {
-                stroke: 'var(--border-primary)',
-                strokeWidth: 2,
-              },
-            });
-          }
+        if (childArtifact && !visited.has(childArtifact.artifact_id)) {
+          children.push(buildNode(childArtifact, depth + 1));
         }
       }
 
-      return nodeId;
+      return {
+        id: nodeId,
+        project: artifact.project,
+        package: artifact.package,
+        version: artifact.version || artifact.tag,
+        size: artifact.size,
+        depth,
+        children,
+        isRoot: depth === 0,
+      };
     };
 
-    processNode(rootArtifact, true);
-
-    // Apply dagre layout
-    return getLayoutedElements(flowNodes, flowEdges);
+    return buildNode(rootArtifact, 0);
   }, []);
 
   useEffect(() => {
@@ -222,21 +117,13 @@ function DependencyGraph({ projectName, packageName, tagName, onClose }: Depende
 
       try {
         const result = await resolveDependencies(projectName, packageName, tagName);
-
-        // If only the root package (no dependencies) and no missing deps, close the modal
-        const hasDeps = result.artifact_count > 1 || (result.missing && result.missing.length > 0);
-        if (!hasDeps) {
-          onClose();
-          return;
-        }
-
         setResolution(result);
 
-        const { nodes: layoutedNodes, edges: layoutedEdges } = await buildFlowGraph(result, handleNavigate);
-        setNodes(layoutedNodes);
-        setEdges(layoutedEdges);
+        const graph = await buildGraph(result);
+        setGraphRoot(graph);
       } catch (err) {
         if (err instanceof Error) {
+          // Check if it's a resolution error
           try {
             const errorData = JSON.parse(err.message);
             if (errorData.error === 'circular_dependency') {
@@ -258,9 +145,95 @@ function DependencyGraph({ projectName, packageName, tagName, onClose }: Depende
     }
 
     loadData();
-  }, [projectName, packageName, tagName, buildFlowGraph, handleNavigate, onClose, setNodes, setEdges]);
+  }, [projectName, packageName, tagName, buildGraph]);
 
-  const defaultViewport = useMemo(() => ({ x: 50, y: 50, zoom: 0.8 }), []);
+  const handleNodeClick = (node: GraphNode) => {
+    navigate(`/project/${node.project}/${node.package}`);
+    onClose();
+  };
+
+  const handleNodeToggle = (node: GraphNode, e: React.MouseEvent) => {
+    e.stopPropagation();
+    setCollapsedNodes(prev => {
+      const next = new Set(prev);
+      if (next.has(node.id)) {
+        next.delete(node.id);
+      } else {
+        next.add(node.id);
+      }
+      return next;
+    });
+  };
+
+  const handleWheel = (e: React.WheelEvent) => {
+    e.preventDefault();
+    const delta = e.deltaY > 0 ? -0.1 : 0.1;
+    setZoom(z => Math.max(0.25, Math.min(2, z + delta)));
+  };
+
+  const handleMouseDown = (e: React.MouseEvent) => {
+    if (e.target === containerRef.current || (e.target as HTMLElement).classList.contains('graph-canvas')) {
+      setIsDragging(true);
+      setDragStart({ x: e.clientX - pan.x, y: e.clientY - pan.y });
+    }
+  };
+
+  const handleMouseMove = (e: React.MouseEvent) => {
+    if (isDragging) {
+      setPan({ x: e.clientX - dragStart.x, y: e.clientY - dragStart.y });
+    }
+  };
+
+  const handleMouseUp = () => {
+    setIsDragging(false);
+  };
+
+  const resetView = () => {
+    setZoom(1);
+    setPan({ x: 0, y: 0 });
+  };
+
+  const renderNode = (node: GraphNode, index: number = 0): JSX.Element => {
+    const isCollapsed = collapsedNodes.has(node.id);
+    const hasChildren = node.children.length > 0;
+
+    return (
+      <div key={`${node.id}-${index}`} className="graph-node-container">
+        <div
+          className={`graph-node ${node.isRoot ? 'graph-node--root' : ''} ${hoveredNode?.id === node.id ? 'graph-node--hovered' : ''}`}
+          onClick={() => handleNodeClick(node)}
+          onMouseEnter={() => setHoveredNode(node)}
+          onMouseLeave={() => setHoveredNode(null)}
+        >
+          <div className="graph-node__header">
+            <span className="graph-node__name">{node.project}/{node.package}</span>
+            {hasChildren && (
+              <button
+                className="graph-node__toggle"
+                onClick={(e) => handleNodeToggle(node, e)}
+                title={isCollapsed ? 'Expand' : 'Collapse'}
+              >
+                {isCollapsed ? '+' : '-'}
+              </button>
+            )}
+          </div>
+          <div className="graph-node__details">
+            {node.version && <span className="graph-node__version">@ {node.version}</span>}
+            <span className="graph-node__size">{formatBytes(node.size)}</span>
+          </div>
+        </div>
+
+        {hasChildren && !isCollapsed && (
+          <div className="graph-children">
+            <div className="graph-connector"></div>
+            <div className="graph-children-list">
+              {node.children.map((child, i) => renderNode(child, i))}
+            </div>
+          </div>
+        )}
+      </div>
+    );
+  };
 
   return (
     <div className="dependency-graph-modal" onClick={onClose}>
@@ -271,11 +244,7 @@ function DependencyGraph({ projectName, packageName, tagName, onClose }: Depende
             <span>{projectName}/{packageName} @ {tagName}</span>
             {resolution && (
               <span className="graph-stats">
-                {resolution.artifact_count} cached
-                {resolution.missing && resolution.missing.length > 0 && (
-                  <span className="missing-count"> • {resolution.missing.length} not cached</span>
-                )}
-                 • {formatBytes(resolution.total_size)} total
+                {resolution.artifact_count} packages • {formatBytes(resolution.total_size)} total
               </span>
             )}
           </div>
@@ -287,7 +256,28 @@ function DependencyGraph({ projectName, packageName, tagName, onClose }: Depende
           </button>
         </div>
 
-        <div className="dependency-graph-container">
+        <div className="dependency-graph-toolbar">
+          <button className="btn btn-secondary btn-small" onClick={() => setZoom(z => Math.min(2, z + 0.25))}>
+            Zoom In
+          </button>
+          <button className="btn btn-secondary btn-small" onClick={() => setZoom(z => Math.max(0.25, z - 0.25))}>
+            Zoom Out
+          </button>
+          <button className="btn btn-secondary btn-small" onClick={resetView}>
+            Reset View
+          </button>
+          <span className="zoom-level">{Math.round(zoom * 100)}%</span>
+        </div>
+
+        <div
+          ref={containerRef}
+          className="dependency-graph-container"
+          onWheel={handleWheel}
+          onMouseDown={handleMouseDown}
+          onMouseMove={handleMouseMove}
+          onMouseUp={handleMouseUp}
+          onMouseLeave={handleMouseUp}
+        >
           {loading ? (
             <div className="graph-loading">
               <div className="spinner"></div>
@@ -302,41 +292,27 @@ function DependencyGraph({ projectName, packageName, tagName, onClose }: Depende
               </svg>
               <p>{error}</p>
             </div>
-          ) : nodes.length > 0 ? (
-            <ReactFlow
-              nodes={nodes}
-              edges={edges}
-              onNodesChange={onNodesChange}
-              onEdgesChange={onEdgesChange}
-              nodeTypes={nodeTypes}
-              defaultViewport={defaultViewport}
-              fitView
-              fitViewOptions={{ padding: 0.2 }}
-              minZoom={0.1}
-              maxZoom={2}
-              attributionPosition="bottom-left"
+          ) : graphRoot ? (
+            <div
+              className="graph-canvas"
+              style={{
+                transform: `translate(${pan.x}px, ${pan.y}px) scale(${zoom})`,
+                cursor: isDragging ? 'grabbing' : 'grab',
+              }}
             >
-              <Controls />
-              <Background color="var(--border-primary)" gap={20} />
-            </ReactFlow>
+              {renderNode(graphRoot)}
+            </div>
           ) : (
             <div className="graph-empty">No dependencies to display</div>
           )}
         </div>
 
-        {resolution && resolution.missing && resolution.missing.length > 0 && (
-          <div className="missing-dependencies">
-            <h3>Not Cached ({resolution.missing.length})</h3>
-            <p className="missing-hint">These dependencies are referenced but not yet cached on the server.</p>
-            <ul className="missing-list">
-              {resolution.missing.map((dep, i) => (
-                <li key={i} className="missing-item">
-                  <span className="missing-name">{dep.project}/{dep.package}</span>
-                  {dep.constraint && <span className="missing-constraint">@{dep.constraint}</span>}
-                  {dep.required_by && <span className="missing-required-by">← {dep.required_by}</span>}
-                </li>
-              ))}
-            </ul>
+        {hoveredNode && (
+          <div className="graph-tooltip">
+            <strong>{hoveredNode.project}/{hoveredNode.package}</strong>
+            {hoveredNode.version && <div>Version: {hoveredNode.version}</div>}
+            <div>Size: {formatBytes(hoveredNode.size)}</div>
+            <div className="tooltip-hint">Click to navigate</div>
           </div>
         )}
       </div>

frontend/src/components/Layout.css

@@ -272,7 +272,7 @@
 .footer {
   background: var(--bg-secondary);
   border-top: 1px solid var(--border-primary);
-  padding: 12px 0;
+  padding: 24px 0;
 }
 
 .footer-content {

frontend/src/components/Layout.tsx

@@ -84,6 +84,29 @@ function Layout({ children }: LayoutProps) {
               </svg>
               Projects
             </Link>
+            <Link to="/dashboard" className={location.pathname === '/dashboard' ? 'active' : ''}>
+              <svg width="16" height="16" viewBox="0 0 24 24" fill="none" stroke="currentColor" strokeWidth="2">
+                <rect x="3" y="3" width="7" height="7" rx="1"/>
+                <rect x="14" y="3" width="7" height="7" rx="1"/>
+                <rect x="3" y="14" width="7" height="7" rx="1"/>
+                <rect x="14" y="14" width="7" height="7" rx="1"/>
+              </svg>
+              Dashboard
+            </Link>
+            {user && userTeams.length > 0 && (
+              <Link
+                to={userTeams.length === 1 ? `/teams/${userTeams[0].slug}` : '/teams'}
+                className={location.pathname.startsWith('/teams') ? 'active' : ''}
+              >
+                <svg width="16" height="16" viewBox="0 0 24 24" fill="none" stroke="currentColor" strokeWidth="2">
+                  <path d="M17 21v-2a4 4 0 0 0-4-4H5a4 4 0 0 0-4 4v2"/>
+                  <circle cx="9" cy="7" r="4"/>
+                  <path d="M23 21v-2a4 4 0 0 0-3-3.87"/>
+                  <path d="M16 3.13a4 4 0 0 1 0 7.75"/>
+                </svg>
+                {userTeams.length === 1 ? 'Team' : 'Teams'}
+              </Link>
+            )}
             <a href="/docs" className="nav-link-muted">
               <svg width="16" height="16" viewBox="0 0 24 24" fill="none" stroke="currentColor" strokeWidth="2">
                 <path d="M14 2H6a2 2 0 0 0-2 2v16a2 2 0 0 0 2 2h12a2 2 0 0 0 2-2V8z"/>
@@ -125,35 +148,6 @@ function Layout({ children }: LayoutProps) {
                       )}
                     </div>
                     <div className="user-menu-divider"></div>
-                    <NavLink
-                      to="/dashboard"
-                      className="user-menu-item"
-                      onClick={() => setShowUserMenu(false)}
-                    >
-                      <svg width="16" height="16" viewBox="0 0 24 24" fill="none" stroke="currentColor" strokeWidth="2">
-                        <rect x="3" y="3" width="7" height="7" rx="1"/>
-                        <rect x="14" y="3" width="7" height="7" rx="1"/>
-                        <rect x="3" y="14" width="7" height="7" rx="1"/>
-                        <rect x="14" y="14" width="7" height="7" rx="1"/>
-                      </svg>
-                      Dashboard
-                    </NavLink>
-                    {userTeams.length > 0 && (
-                      <NavLink
-                        to={userTeams.length === 1 ? `/teams/${userTeams[0].slug}` : '/teams'}
-                        className="user-menu-item"
-                        onClick={() => setShowUserMenu(false)}
-                      >
-                        <svg width="16" height="16" viewBox="0 0 24 24" fill="none" stroke="currentColor" strokeWidth="2">
-                          <path d="M17 21v-2a4 4 0 0 0-4-4H5a4 4 0 0 0-4 4v2"/>
-                          <circle cx="9" cy="7" r="4"/>
-                          <path d="M23 21v-2a4 4 0 0 0-3-3.87"/>
-                          <path d="M16 3.13a4 4 0 0 1 0 7.75"/>
-                        </svg>
-                        {userTeams.length === 1 ? 'Team' : 'Teams'}
-                      </NavLink>
-                    )}
-                    <div className="user-menu-divider"></div>
                     <NavLink
                       to="/settings/api-keys"
                       className="user-menu-item"

frontend/src/pages/AdminCachePage.css

@@ -34,6 +34,74 @@
   margin-bottom: 1rem;
 }
 
+/* Settings Section */
+.settings-section {
+  background: var(--bg-secondary);
+  border: 1px solid var(--border-color);
+  border-radius: 8px;
+  padding: 1.5rem;
+  margin-bottom: 2rem;
+}
+
+.settings-grid {
+  display: flex;
+  flex-direction: column;
+  gap: 1rem;
+}
+
+.setting-item {
+  display: flex;
+  justify-content: space-between;
+  align-items: center;
+  padding: 1rem;
+  background: var(--bg-primary);
+  border: 1px solid var(--border-color);
+  border-radius: 4px;
+}
+
+.toggle-label {
+  display: flex;
+  flex-direction: column;
+  gap: 0.25rem;
+}
+
+.setting-name {
+  font-weight: 500;
+  color: var(--text-primary);
+  display: flex;
+  align-items: center;
+  gap: 0.5rem;
+}
+
+.setting-description {
+  font-size: 0.85rem;
+  color: var(--text-secondary);
+}
+
+.toggle-button {
+  padding: 0.5rem 1rem;
+  border: none;
+  border-radius: 4px;
+  cursor: pointer;
+  font-weight: 500;
+  min-width: 100px;
+}
+
+.toggle-button.on {
+  background-color: #28a745;
+  color: white;
+}
+
+.toggle-button.off {
+  background-color: #dc3545;
+  color: white;
+}
+
+.toggle-button:disabled {
+  opacity: 0.6;
+  cursor: not-allowed;
+}
+
 /* Sources Section */
 .sources-section {
   background: var(--bg-secondary);
@@ -65,7 +133,7 @@
 .sources-table th,
 .sources-table td {
   padding: 0.75rem 1rem;
-  text-align: center;
+  text-align: left;
   border-bottom: 1px solid var(--border-color);
 }
 
@@ -91,11 +159,6 @@
   white-space: nowrap;
 }
 
-/* Name column should be left-aligned */
-.sources-table td:first-child {
-  text-align: left;
-}
-
 .url-cell {
   font-family: monospace;
   font-size: 0.9rem;
@@ -103,7 +166,6 @@
   overflow: hidden;
   text-overflow: ellipsis;
   white-space: nowrap;
-  text-align: left;
 }
 
 /* Badges */
@@ -132,12 +194,6 @@
   color: #c62828;
 }
 
-.coming-soon-badge {
-  color: #9e9e9e;
-  font-style: italic;
-  font-size: 0.85em;
-}
-
 /* Actions */
 .actions-cell {
   white-space: nowrap;
@@ -151,37 +207,35 @@
   margin-right: 0;
 }
 
-.test-cell {
-  text-align: center;
-  width: 2rem;
+.test-result {
+  display: inline-flex;
+  align-items: center;
+  gap: 0.25rem;
+  padding: 0.2rem 0.5rem;
+  border-radius: 4px;
+  font-size: 0.75rem;
+  font-weight: 500;
+  white-space: nowrap;
 }
 
-.test-dot {
-  font-size: 1rem;
-  cursor: default;
-}
-
-.test-dot.success {
+.test-result.success {
+  background-color: #e8f5e9;
   color: #2e7d32;
 }
 
-.test-dot.failure {
+.test-result.failure {
+  background-color: #ffebee;
   color: #c62828;
   cursor: pointer;
 }
 
-.test-dot.failure:hover {
-  color: #b71c1c;
+.test-result.failure:hover {
+  background-color: #ffcdd2;
 }
 
-.test-dot.testing {
+.test-result.testing {
+  background-color: #e3f2fd;
   color: #1976d2;
-  animation: pulse 1s infinite;
-}
-
-@keyframes pulse {
-  0%, 100% { opacity: 1; }
-  50% { opacity: 0.4; }
 }
 
 /* Error Modal */
@@ -255,22 +309,10 @@
 }
 
 .btn-sm {
-  padding: 0.25rem 0.75rem;
+  padding: 0.25rem 0.5rem;
   font-size: 0.8rem;
 }
 
-.btn-secondary {
-  background-color: var(--bg-tertiary);
-  border-color: var(--border-color);
-  color: var(--text-primary);
-  font-weight: 500;
-}
-
-.btn-secondary:hover {
-  background-color: var(--bg-secondary);
-  border-color: var(--text-secondary);
-}
-
 .empty-message {
   color: var(--text-secondary);
   font-style: italic;
@@ -364,14 +406,9 @@
 
 .form-actions {
   display: flex;
-  justify-content: space-between;
-  align-items: center;
+  justify-content: flex-end;
+  gap: 0.5rem;
   margin-top: 1.5rem;
   padding-top: 1rem;
   border-top: 1px solid var(--border-color);
 }
-
-.form-actions-right {
-  display: flex;
-  gap: 0.5rem;
-}

frontend/src/pages/AdminCachePage.tsx

@@ -7,12 +7,13 @@ import {
   updateUpstreamSource,
   deleteUpstreamSource,
   testUpstreamSource,
+  getCacheSettings,
+  updateCacheSettings,
 } from '../api';
-import { UpstreamSource, SourceType, AuthType } from '../types';
+import { UpstreamSource, CacheSettings, SourceType, AuthType } from '../types';
 import './AdminCachePage.css';
 
 const SOURCE_TYPES: SourceType[] = ['npm', 'pypi', 'maven', 'docker', 'helm', 'nuget', 'deb', 'rpm', 'generic'];
-const SUPPORTED_SOURCE_TYPES: Set<SourceType> = new Set(['pypi', 'generic']);
 const AUTH_TYPES: AuthType[] = ['none', 'basic', 'bearer', 'api_key'];
 
 function AdminCachePage() {
@@ -24,6 +25,11 @@ function AdminCachePage() {
   const [loadingSources, setLoadingSources] = useState(true);
   const [sourcesError, setSourcesError] = useState<string | null>(null);
 
+  // Cache settings state
+  const [settings, setSettings] = useState<CacheSettings | null>(null);
+  const [loadingSettings, setLoadingSettings] = useState(true);
+  const [settingsError, setSettingsError] = useState<string | null>(null);
+
   // Create/Edit form state
   const [showForm, setShowForm] = useState(false);
   const [editingSource, setEditingSource] = useState<UpstreamSource | null>(null);
@@ -47,6 +53,9 @@ function AdminCachePage() {
   // Delete confirmation state
   const [deletingId, setDeletingId] = useState<string | null>(null);
 
+  // Settings update state
+  const [updatingSettings, setUpdatingSettings] = useState(false);
+
   // Success message
   const [successMessage, setSuccessMessage] = useState<string | null>(null);
 
@@ -63,6 +72,7 @@ function AdminCachePage() {
   useEffect(() => {
     if (user && user.is_admin) {
       loadSources();
+      loadSettings();
     }
   }, [user]);
 
@@ -86,6 +96,19 @@ function AdminCachePage() {
     }
   }
 
+  async function loadSettings() {
+    setLoadingSettings(true);
+    setSettingsError(null);
+    try {
+      const data = await getCacheSettings();
+      setSettings(data);
+    } catch (err) {
+      setSettingsError(err instanceof Error ? err.message : 'Failed to load settings');
+    } finally {
+      setLoadingSettings(false);
+    }
+  }
+
   function openCreateForm() {
     setEditingSource(null);
     setFormData({
@@ -232,6 +255,30 @@ function AdminCachePage() {
     setShowErrorModal(true);
   }
 
+  async function handleSettingsToggle(field: 'auto_create_system_projects') {
+    if (!settings) return;
+
+    // Check if env override is active
+    const isOverridden = field === 'auto_create_system_projects' && settings.auto_create_system_projects_env_override !== null;
+
+    if (isOverridden) {
+      alert('This setting is overridden by an environment variable and cannot be changed via UI.');
+      return;
+    }
+
+    setUpdatingSettings(true);
+    try {
+      const update = { [field]: !settings[field] };
+      const newSettings = await updateCacheSettings(update);
+      setSettings(newSettings);
+      setSuccessMessage(`Setting "${field}" updated`);
+    } catch (err) {
+      setSettingsError(err instanceof Error ? err.message : 'Failed to update settings');
+    } finally {
+      setUpdatingSettings(false);
+    }
+  }
+
   if (authLoading) {
     return <div className="admin-cache-page">Loading...</div>;
   }
@@ -246,13 +293,49 @@ function AdminCachePage() {
 
   return (
     <div className="admin-cache-page">
-      <h1>Upstream Sources</h1>
+      <h1>Cache Management</h1>
 
       {successMessage && <div className="success-message">{successMessage}</div>}
 
+      {/* Cache Settings Section */}
+      <section className="settings-section">
+        <h2>Global Settings</h2>
+        {loadingSettings ? (
+          <p>Loading settings...</p>
+        ) : settingsError ? (
+          <div className="error-message">{settingsError}</div>
+        ) : settings ? (
+          <div className="settings-grid">
+            <div className="setting-item">
+              <label className="toggle-label">
+                <span className="setting-name">
+                  Auto-create System Projects
+                  {settings.auto_create_system_projects_env_override !== null && (
+                    <span className="env-badge" title="Overridden by environment variable">
+                      ENV
+                    </span>
+                  )}
+                </span>
+                <span className="setting-description">
+                  Automatically create system projects (_npm, _pypi, etc.) on first cache request.
+                </span>
+              </label>
+              <button
+                className={`toggle-button ${settings.auto_create_system_projects ? 'on' : 'off'}`}
+                onClick={() => handleSettingsToggle('auto_create_system_projects')}
+                disabled={updatingSettings || settings.auto_create_system_projects_env_override !== null}
+              >
+                {settings.auto_create_system_projects ? 'Enabled' : 'Disabled'}
+              </button>
+            </div>
+          </div>
+        ) : null}
+      </section>
+
       {/* Upstream Sources Section */}
       <section className="sources-section">
         <div className="section-header">
+          <h2>Upstream Sources</h2>
           <button className="btn btn-primary" onClick={openCreateForm}>
             Add Source
           </button>
@@ -273,6 +356,7 @@ function AdminCachePage() {
                 <th>URL</th>
                 <th>Priority</th>
                 <th>Status</th>
+                <th>Source</th>
                 <th>Test</th>
                 <th>Actions</th>
               </tr>
@@ -282,50 +366,66 @@ function AdminCachePage() {
                 <tr key={source.id} className={source.enabled ? '' : 'disabled-row'}>
                   <td>
                     <span className="source-name">{source.name}</span>
-                    {source.source === 'env' && (
-                      <span className="env-badge" title="Defined via environment variable">ENV</span>
-                    )}
                   </td>
-                  <td>
-                    {source.source_type}
-                    {!SUPPORTED_SOURCE_TYPES.has(source.source_type) && (
-                      <span className="coming-soon-badge"> (coming soon)</span>
-                    )}
-                  </td>
-                  <td className="url-cell" title={source.url}>{source.url}</td>
+                  <td>{source.source_type}</td>
+                  <td className="url-cell">{source.url}</td>
                   <td>{source.priority}</td>
                   <td>
                     <span className={`status-badge ${source.enabled ? 'enabled' : 'disabled'}`}>
                       {source.enabled ? 'Enabled' : 'Disabled'}
                     </span>
                   </td>
-                  <td className="test-cell">
+                  <td>
+                    {source.source === 'env' ? (
+                      <span className="env-badge" title="Defined via environment variable">
+                        ENV
+                      </span>
+                    ) : (
+                      'Database'
+                    )}
+                  </td>
+                  <td>
                     {testingId === source.id ? (
-                      <span className="test-dot testing" title="Testing...">●</span>
+                      <span className="test-result testing">Testing...</span>
                     ) : testResults[source.id] ? (
                       testResults[source.id].success ? (
-                        <span className="test-dot success" title={testResults[source.id].message}>●</span>
+                        <span className="test-result success" title={testResults[source.id].message}>
+                          OK
+                        </span>
                       ) : (
                         <span
-                          className="test-dot failure"
-                          title="Click to see error"
+                          className="test-result failure"
+                          title="Click to see details"
                           onClick={() => showError(source.name, testResults[source.id].message)}
-                        >●</span>
+                        >
+                          Error
+                        </span>
                       )
-                    ) : null}
+                    ) : (
+                      <span className="test-result" style={{ opacity: 0.5 }}>—</span>
+                    )}
                   </td>
                   <td className="actions-cell">
                     <button
-                      className="btn btn-sm btn-secondary"
+                      className="btn btn-sm"
                       onClick={() => handleTest(source)}
                       disabled={testingId === source.id}
                     >
                       Test
                     </button>
                     {source.source !== 'env' && (
-                      <button className="btn btn-sm btn-secondary" onClick={() => openEditForm(source)}>
-                        Edit
-                      </button>
+                      <>
+                        <button className="btn btn-sm" onClick={() => openEditForm(source)}>
+                          Edit
+                        </button>
+                        <button
+                          className="btn btn-sm btn-danger"
+                          onClick={() => handleDelete(source)}
+                          disabled={deletingId === source.id}
+                        >
+                          {deletingId === source.id ? 'Deleting...' : 'Delete'}
+                        </button>
+                      </>
                     )}
                   </td>
                 </tr>
@@ -365,7 +465,7 @@ function AdminCachePage() {
                   >
                     {SOURCE_TYPES.map((type) => (
                       <option key={type} value={type}>
-                        {type}{!SUPPORTED_SOURCE_TYPES.has(type) ? ' (coming soon)' : ''}
+                        {type}
                       </option>
                     ))}
                   </select>
@@ -461,27 +561,12 @@ function AdminCachePage() {
               )}
 
               <div className="form-actions">
-                {editingSource && (
-                  <button
-                    type="button"
-                    className="btn btn-danger"
-                    onClick={() => {
-                      handleDelete(editingSource);
-                      setShowForm(false);
-                    }}
-                    disabled={deletingId === editingSource.id}
-                  >
-                    {deletingId === editingSource.id ? 'Deleting...' : 'Delete'}
-                  </button>
-                )}
-                <div className="form-actions-right">
-                  <button type="button" className="btn" onClick={() => setShowForm(false)}>
-                    Cancel
-                  </button>
-                  <button type="submit" className="btn btn-primary" disabled={isSaving}>
-                    {isSaving ? 'Saving...' : editingSource ? 'Update' : 'Create'}
-                  </button>
-                </div>
+                <button type="button" className="btn" onClick={() => setShowForm(false)}>
+                  Cancel
+                </button>
+                <button type="submit" className="btn btn-primary" disabled={isSaving}>
+                  {isSaving ? 'Saving...' : editingSource ? 'Update' : 'Create'}
+                </button>
               </div>
             </form>
           </div>

frontend/src/pages/Home.tsx

@@ -249,7 +249,7 @@ function Home() {
               key: 'created_by',
               header: 'Owner',
               className: 'cell-owner',
-              render: (project) => project.team_name || project.created_by,
+              render: (project) => project.created_by,
             },
             ...(user
               ? [

frontend/src/pages/PackagePage.css

@@ -642,11 +642,6 @@ tr:hover .copy-btn {
   padding: 20px;
 }
 
-/* Ensure file modal needs higher z-index when opened from deps modal */
-.modal-overlay:has(.ensure-file-modal) {
-  z-index: 1100;
-}
-
 .ensure-file-modal {
   background: var(--bg-secondary);
   border: 1px solid var(--border-primary);
@@ -798,194 +793,4 @@ tr:hover .copy-btn {
   .ensure-file-modal {
     max-height: 90vh;
   }
-
-  .action-menu-dropdown {
-    right: 0;
-    left: auto;
-  }
-}
-
-/* Header upload button */
-.header-upload-btn {
-  margin-left: auto;
-}
-
-/* Tag/Version cell */
-.tag-version-cell {
-  display: flex;
-  flex-direction: column;
-  gap: 4px;
-}
-
-.tag-version-cell .version-badge {
-  font-size: 0.75rem;
-  color: var(--text-muted);
-}
-
-/* Icon buttons */
-.btn-icon {
-  display: flex;
-  align-items: center;
-  justify-content: center;
-  width: 32px;
-  height: 32px;
-  padding: 0;
-  background: transparent;
-  border: 1px solid transparent;
-  border-radius: var(--radius-sm);
-  color: var(--text-secondary);
-  cursor: pointer;
-  transition: all var(--transition-fast);
-}
-
-.btn-icon:hover {
-  background: var(--bg-hover);
-  color: var(--text-primary);
-}
-
-/* Action menu */
-.action-buttons {
-  display: flex;
-  align-items: center;
-  gap: 4px;
-}
-
-.action-menu {
-  position: relative;
-}
-
-/* Action menu backdrop for click-outside */
-.action-menu-backdrop {
-  position: fixed;
-  top: 0;
-  left: 0;
-  right: 0;
-  bottom: 0;
-  z-index: 999;
-}
-
-.action-menu-dropdown {
-  position: fixed;
-  z-index: 1000;
-  min-width: 180px;
-  padding: 4px 0;
-  background: var(--bg-secondary);
-  border: 1px solid var(--border-primary);
-  border-radius: var(--radius-md);
-  box-shadow: 0 4px 12px rgba(0, 0, 0, 0.15);
-}
-
-.action-menu-dropdown button {
-  display: block;
-  width: 100%;
-  padding: 8px 12px;
-  background: none;
-  border: none;
-  text-align: left;
-  font-size: 0.875rem;
-  color: var(--text-primary);
-  cursor: pointer;
-  transition: background var(--transition-fast);
-}
-
-.action-menu-dropdown button:hover {
-  background: var(--bg-hover);
-}
-
-/* Upload Modal */
-.upload-modal,
-.create-tag-modal {
-  background: var(--bg-secondary);
-  border-radius: var(--radius-lg);
-  width: 90%;
-  max-width: 500px;
-  max-height: 90vh;
-  overflow: hidden;
-}
-
-.modal-header {
-  display: flex;
-  align-items: center;
-  justify-content: space-between;
-  padding: 16px 20px;
-  border-bottom: 1px solid var(--border-primary);
-}
-
-.modal-header h3 {
-  margin: 0;
-  font-size: 1.125rem;
-  font-weight: 600;
-}
-
-.modal-body {
-  padding: 20px;
-}
-
-.modal-description {
-  margin-bottom: 16px;
-  color: var(--text-secondary);
-  font-size: 0.875rem;
-}
-
-.modal-actions {
-  display: flex;
-  justify-content: flex-end;
-  gap: 12px;
-  margin-top: 20px;
-  padding-top: 16px;
-  border-top: 1px solid var(--border-primary);
-}
-
-/* Dependencies Modal */
-.deps-modal {
-  background: var(--bg-secondary);
-  border-radius: var(--radius-lg);
-  width: 90%;
-  max-width: 600px;
-  max-height: 80vh;
-  overflow: hidden;
-  display: flex;
-  flex-direction: column;
-}
-
-.deps-modal .modal-body {
-  overflow-y: auto;
-  flex: 1;
-}
-
-.deps-modal-controls {
-  display: flex;
-  gap: 8px;
-  margin-bottom: 16px;
-}
-
-/* Artifact ID Modal */
-.artifact-id-modal {
-  background: var(--bg-secondary);
-  border-radius: var(--radius-lg);
-  width: 90%;
-  max-width: 500px;
-}
-
-.artifact-id-display {
-  display: flex;
-  align-items: center;
-  gap: 12px;
-  padding: 16px;
-  background: var(--bg-tertiary);
-  border-radius: var(--radius-md);
-  border: 1px solid var(--border-primary);
-}
-
-.artifact-id-display code {
-  font-family: 'JetBrains Mono', 'Fira Code', 'Consolas', monospace;
-  font-size: 0.8125rem;
-  color: var(--text-primary);
-  word-break: break-all;
-  flex: 1;
-}
-
-.artifact-id-display .copy-btn {
-  opacity: 1;
-  flex-shrink: 0;
 }

frontend/src/pages/PackagePage.tsx

@@ -63,17 +63,12 @@ function PackagePage() {
   const [accessDenied, setAccessDenied] = useState(false);
   const [uploadTag, setUploadTag] = useState('');
   const [uploadSuccess, setUploadSuccess] = useState<string | null>(null);
+  const [artifactIdInput, setArtifactIdInput] = useState('');
   const [accessLevel, setAccessLevel] = useState<AccessLevel | null>(null);
   const [createTagName, setCreateTagName] = useState('');
   const [createTagArtifactId, setCreateTagArtifactId] = useState('');
   const [createTagLoading, setCreateTagLoading] = useState(false);
 
-  // UI state
-  const [showUploadModal, setShowUploadModal] = useState(false);
-  const [showCreateTagModal, setShowCreateTagModal] = useState(false);
-  const [openMenuId, setOpenMenuId] = useState<string | null>(null);
-  const [menuPosition, setMenuPosition] = useState<{ top: number; left: number } | null>(null);
-
   // Dependencies state
   const [selectedTag, setSelectedTag] = useState<TagDetail | null>(null);
   const [dependencies, setDependencies] = useState<Dependency[]>([]);
@@ -83,7 +78,7 @@ function PackagePage() {
   // Reverse dependencies state
   const [reverseDeps, setReverseDeps] = useState<DependentInfo[]>([]);
   const [reverseDepsLoading, setReverseDepsLoading] = useState(false);
-  const [_reverseDepsError, setReverseDepsError] = useState<string | null>(null);
+  const [reverseDepsError, setReverseDepsError] = useState<string | null>(null);
   const [reverseDepsPage, setReverseDepsPage] = useState(1);
   const [reverseDepsTotal, setReverseDepsTotal] = useState(0);
   const [reverseDepsHasMore, setReverseDepsHasMore] = useState(false);
@@ -91,13 +86,6 @@ function PackagePage() {
   // Dependency graph modal state
   const [showGraph, setShowGraph] = useState(false);
 
-  // Dependencies modal state
-  const [showDepsModal, setShowDepsModal] = useState(false);
-
-  // Artifact ID modal state
-  const [showArtifactIdModal, setShowArtifactIdModal] = useState(false);
-  const [viewArtifactId, setViewArtifactId] = useState<string | null>(null);
-
   // Ensure file modal state
   const [showEnsureFile, setShowEnsureFile] = useState(false);
   const [ensureFileContent, setEnsureFileContent] = useState<string | null>(null);
@@ -108,9 +96,6 @@ function PackagePage() {
   // Derived permissions
   const canWrite = accessLevel === 'write' || accessLevel === 'admin';
 
-  // Detect system projects (convention: name starts with "_")
-  const isSystemProject = projectName?.startsWith('_') ?? false;
-
   // Get params from URL
   const page = parseInt(searchParams.get('page') || '1', 10);
   const search = searchParams.get('search') || '';
@@ -338,212 +323,92 @@ function PackagePage() {
     setSelectedTag(tag);
   };
 
-  const handleMenuOpen = (e: React.MouseEvent, tagId: string) => {
-    e.stopPropagation();
-    if (openMenuId === tagId) {
-      setOpenMenuId(null);
-      setMenuPosition(null);
-    } else {
-      const rect = e.currentTarget.getBoundingClientRect();
-      setMenuPosition({ top: rect.bottom + 4, left: rect.right - 180 });
-      setOpenMenuId(tagId);
-    }
-  };
-
-  // System projects show Version first, regular projects show Tag first
-  const columns = isSystemProject
-    ? [
-        // System project columns: Version first, then Filename
-        {
-          key: 'version',
-          header: 'Version',
-          sortable: true,
-          render: (t: TagDetail) => (
-            <strong
-              className={`tag-name-link ${selectedTag?.id === t.id ? 'selected' : ''}`}
-              onClick={() => handleTagSelect(t)}
-              style={{ cursor: 'pointer' }}
-            >
-              <span className="version-badge">{t.version || t.name}</span>
-            </strong>
-          ),
-        },
-        {
-          key: 'artifact_original_name',
-          header: 'Filename',
-          className: 'cell-truncate',
-          render: (t: TagDetail) => (
-            <span title={t.artifact_original_name || t.name}>{t.artifact_original_name || t.name}</span>
-          ),
-        },
-        {
-          key: 'artifact_size',
-          header: 'Size',
-          render: (t: TagDetail) => <span>{formatBytes(t.artifact_size)}</span>,
-        },
-        {
-          key: 'created_at',
-          header: 'Cached',
-          sortable: true,
-          render: (t: TagDetail) => (
-            <span>{new Date(t.created_at).toLocaleDateString()}</span>
-          ),
-        },
-        {
-          key: 'actions',
-          header: '',
-          render: (t: TagDetail) => (
-            <div className="action-buttons">
-              <a
-                href={getDownloadUrl(projectName!, packageName!, t.name)}
-                className="btn btn-icon"
-                download
-                title="Download"
-              >
-                <svg width="16" height="16" viewBox="0 0 24 24" fill="none" stroke="currentColor" strokeWidth="2">
-                  <path d="M21 15v4a2 2 0 0 1-2 2H5a2 2 0 0 1-2-2v-4" />
-                  <polyline points="7 10 12 15 17 10" />
-                  <line x1="12" y1="15" x2="12" y2="3" />
-                </svg>
-              </a>
-              <button
-                className="btn btn-icon"
-                onClick={(e) => handleMenuOpen(e, t.id)}
-                title="More actions"
-              >
-                <svg width="16" height="16" viewBox="0 0 24 24" fill="none" stroke="currentColor" strokeWidth="2">
-                  <circle cx="12" cy="12" r="1" />
-                  <circle cx="12" cy="5" r="1" />
-                  <circle cx="12" cy="19" r="1" />
-                </svg>
-              </button>
-            </div>
-          ),
-        },
-      ]
-    : [
-        // Regular project columns: Tag, Version, Filename
-        {
-          key: 'name',
-          header: 'Tag',
-          sortable: true,
-          render: (t: TagDetail) => (
-            <strong
-              className={`tag-name-link ${selectedTag?.id === t.id ? 'selected' : ''}`}
-              onClick={() => handleTagSelect(t)}
-              style={{ cursor: 'pointer' }}
-            >
-              {t.name}
-            </strong>
-          ),
-        },
-        {
-          key: 'version',
-          header: 'Version',
-          render: (t: TagDetail) => (
-            <span className="version-badge">{t.version || '—'}</span>
-          ),
-        },
-        {
-          key: 'artifact_original_name',
-          header: 'Filename',
-          className: 'cell-truncate',
-          render: (t: TagDetail) => (
-            <span title={t.artifact_original_name || undefined}>{t.artifact_original_name || '—'}</span>
-          ),
-        },
-        {
-          key: 'artifact_size',
-          header: 'Size',
-          render: (t: TagDetail) => <span>{formatBytes(t.artifact_size)}</span>,
-        },
-        {
-          key: 'created_at',
-          header: 'Created',
-          sortable: true,
-          render: (t: TagDetail) => (
-            <span title={`by ${t.created_by}`}>{new Date(t.created_at).toLocaleDateString()}</span>
-          ),
-        },
-        {
-          key: 'actions',
-          header: '',
-          render: (t: TagDetail) => (
-            <div className="action-buttons">
-              <a
-                href={getDownloadUrl(projectName!, packageName!, t.name)}
-                className="btn btn-icon"
-                download
-                title="Download"
-              >
-                <svg width="16" height="16" viewBox="0 0 24 24" fill="none" stroke="currentColor" strokeWidth="2">
-                  <path d="M21 15v4a2 2 0 0 1-2 2H5a2 2 0 0 1-2-2v-4" />
-                  <polyline points="7 10 12 15 17 10" />
-                  <line x1="12" y1="15" x2="12" y2="3" />
-                </svg>
-              </a>
-              <button
-                className="btn btn-icon"
-                onClick={(e) => handleMenuOpen(e, t.id)}
-                title="More actions"
-              >
-                <svg width="16" height="16" viewBox="0 0 24 24" fill="none" stroke="currentColor" strokeWidth="2">
-                  <circle cx="12" cy="12" r="1" />
-                  <circle cx="12" cy="5" r="1" />
-                  <circle cx="12" cy="19" r="1" />
-                </svg>
-              </button>
-            </div>
-          ),
-        },
-      ];
-
-  // Find the tag for the open menu
-  const openMenuTag = tags.find(t => t.id === openMenuId);
-
-  // Close menu when clicking outside
-  const handleClickOutside = () => {
-    if (openMenuId) {
-      setOpenMenuId(null);
-      setMenuPosition(null);
-    }
-  };
-
-  // Render dropdown menu as a portal-like element
-  const renderActionMenu = () => {
-    if (!openMenuId || !menuPosition || !openMenuTag) return null;
-    const t = openMenuTag;
-    return (
-      <div
-        className="action-menu-backdrop"
-        onClick={handleClickOutside}
-      >
-        <div
-          className="action-menu-dropdown"
-          style={{ top: menuPosition.top, left: menuPosition.left }}
-          onClick={(e) => e.stopPropagation()}
+  const columns = [
+    {
+      key: 'name',
+      header: 'Tag',
+      sortable: true,
+      render: (t: TagDetail) => (
+        <strong
+          className={`tag-name-link ${selectedTag?.id === t.id ? 'selected' : ''}`}
+          onClick={() => handleTagSelect(t)}
+          style={{ cursor: 'pointer' }}
         >
-          <button onClick={() => { setViewArtifactId(t.artifact_id); setShowArtifactIdModal(true); setOpenMenuId(null); setMenuPosition(null); }}>
-            View Artifact ID
-          </button>
-          <button onClick={() => { navigator.clipboard.writeText(t.artifact_id); setOpenMenuId(null); setMenuPosition(null); }}>
-            Copy Artifact ID
-          </button>
-          <button onClick={() => { fetchEnsureFileForTag(t.name); setOpenMenuId(null); setMenuPosition(null); }}>
-            View Ensure File
-          </button>
-          {canWrite && !isSystemProject && (
-            <button onClick={() => { setCreateTagArtifactId(t.artifact_id); setShowCreateTagModal(true); setOpenMenuId(null); setMenuPosition(null); }}>
-              Create/Update Tag
-            </button>
-          )}
-          <button onClick={() => { handleTagSelect(t); setShowDepsModal(true); setOpenMenuId(null); setMenuPosition(null); }}>
-            View Dependencies
-          </button>
+          {t.name}
+        </strong>
+      ),
+    },
+    {
+      key: 'version',
+      header: 'Version',
+      render: (t: TagDetail) => (
+        <span className="version-badge">{t.version || '-'}</span>
+      ),
+    },
+    {
+      key: 'artifact_id',
+      header: 'Artifact ID',
+      render: (t: TagDetail) => (
+        <div className="artifact-id-cell">
+          <code className="artifact-id">{t.artifact_id.substring(0, 12)}...</code>
+          <CopyButton text={t.artifact_id} />
         </div>
-      </div>
-    );
-  };
+      ),
+    },
+    {
+      key: 'artifact_size',
+      header: 'Size',
+      render: (t: TagDetail) => <span>{formatBytes(t.artifact_size)}</span>,
+    },
+    {
+      key: 'artifact_content_type',
+      header: 'Type',
+      render: (t: TagDetail) => (
+        <span className="content-type">{t.artifact_content_type || '-'}</span>
+      ),
+    },
+    {
+      key: 'artifact_original_name',
+      header: 'Filename',
+      className: 'cell-truncate',
+      render: (t: TagDetail) => (
+        <span title={t.artifact_original_name || undefined}>{t.artifact_original_name || '-'}</span>
+      ),
+    },
+    {
+      key: 'created_at',
+      header: 'Created',
+      sortable: true,
+      render: (t: TagDetail) => (
+        <div className="created-cell">
+          <span>{new Date(t.created_at).toLocaleString()}</span>
+          <span className="created-by">by {t.created_by}</span>
+        </div>
+      ),
+    },
+    {
+      key: 'actions',
+      header: 'Actions',
+      render: (t: TagDetail) => (
+        <div className="action-buttons">
+          <button
+            className="btn btn-secondary btn-small"
+            onClick={() => fetchEnsureFileForTag(t.name)}
+            title="View orchard.ensure file"
+          >
+            Ensure
+          </button>
+          <a
+            href={getDownloadUrl(projectName!, packageName!, t.name)}
+            className="btn btn-secondary btn-small"
+            download
+          >
+            Download
+          </a>
+        </div>
+      ),
+    },
+  ];
 
   if (loading && !tagsData) {
     return <div className="loading">Loading...</div>;
@@ -586,19 +451,6 @@ function PackagePage() {
           <div className="page-header__title-row">
             <h1>{packageName}</h1>
             {pkg && <Badge variant="default">{pkg.format}</Badge>}
-            {user && canWrite && !isSystemProject && (
-              <button
-                className="btn btn-primary btn-small header-upload-btn"
-                onClick={() => setShowUploadModal(true)}
-              >
-                <svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" strokeWidth="2" style={{ marginRight: '6px' }}>
-                  <path d="M21 15v4a2 2 0 0 1-2 2H5a2 2 0 0 1-2-2v-4" />
-                  <polyline points="17 8 12 3 7 8" />
-                  <line x1="12" y1="3" x2="12" y2="15" />
-                </svg>
-                Upload
-              </button>
-            )}
           </div>
           {pkg?.description && <p className="description">{pkg.description}</p>}
           <div className="page-header__meta">
@@ -616,14 +468,14 @@ function PackagePage() {
           </div>
           {pkg && (pkg.tag_count !== undefined || pkg.artifact_count !== undefined) && (
             <div className="package-header-stats">
-              {!isSystemProject && pkg.tag_count !== undefined && (
+              {pkg.tag_count !== undefined && (
                 <span className="stat-item">
                   <strong>{pkg.tag_count}</strong> tags
                 </span>
               )}
               {pkg.artifact_count !== undefined && (
                 <span className="stat-item">
-                  <strong>{pkg.artifact_count}</strong> {isSystemProject ? 'versions' : 'artifacts'}
+                  <strong>{pkg.artifact_count}</strong> artifacts
                 </span>
               )}
               {pkg.total_size !== undefined && pkg.total_size > 0 && (
@@ -631,7 +483,7 @@ function PackagePage() {
                   <strong>{formatBytes(pkg.total_size)}</strong> total
                 </span>
               )}
-              {!isSystemProject && pkg.latest_tag && (
+              {pkg.latest_tag && (
                 <span className="stat-item">
                   Latest: <strong className="accent">{pkg.latest_tag}</strong>
                 </span>
@@ -644,9 +496,44 @@ function PackagePage() {
       {error && <div className="error-message">{error}</div>}
       {uploadSuccess && <div className="success-message">{uploadSuccess}</div>}
 
+      {user && (
+        <div className="upload-section card">
+          <h3>Upload Artifact</h3>
+          {canWrite ? (
+            <div className="upload-form">
+              <div className="form-group">
+                <label htmlFor="upload-tag">Tag (optional)</label>
+                <input
+                  id="upload-tag"
+                  type="text"
+                  value={uploadTag}
+                  onChange={(e) => setUploadTag(e.target.value)}
+                  placeholder="v1.0.0, latest, stable..."
+                />
+              </div>
+              <DragDropUpload
+                projectName={projectName!}
+                packageName={packageName!}
+                tag={uploadTag || undefined}
+                onUploadComplete={handleUploadComplete}
+                onUploadError={handleUploadError}
+              />
+            </div>
+          ) : (
+            <DragDropUpload
+              projectName={projectName!}
+              packageName={packageName!}
+              disabled={true}
+              disabledReason="You have read-only access to this project and cannot upload artifacts."
+              onUploadComplete={handleUploadComplete}
+              onUploadError={handleUploadError}
+            />
+          )}
+        </div>
+      )}
 
       <div className="section-header">
-        <h2>{isSystemProject ? 'Versions' : 'Tags / Versions'}</h2>
+        <h2>Tags / Versions</h2>
       </div>
 
       <div className="list-controls">
@@ -690,10 +577,121 @@ function PackagePage() {
         />
       )}
 
-      {/* Used By (Reverse Dependencies) Section - only show if there are reverse deps */}
-      {reverseDeps.length > 0 && (
-        <div className="used-by-section card">
-          <h3>Used By</h3>
+      {/* Dependencies Section */}
+      {tags.length > 0 && (
+        <div className="dependencies-section card">
+          <div className="dependencies-header">
+            <h3>Dependencies</h3>
+            <div className="dependencies-controls">
+              {selectedTag && (
+                <>
+                  <button
+                    className="btn btn-secondary btn-small"
+                    onClick={fetchEnsureFile}
+                    disabled={ensureFileLoading}
+                    title="View orchard.ensure file"
+                  >
+                    <svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" strokeWidth="2" style={{ marginRight: '6px' }}>
+                      <path d="M14 2H6a2 2 0 0 0-2 2v16a2 2 0 0 0 2 2h12a2 2 0 0 0 2-2V8z"></path>
+                      <polyline points="14 2 14 8 20 8"></polyline>
+                      <line x1="16" y1="13" x2="8" y2="13"></line>
+                      <line x1="16" y1="17" x2="8" y2="17"></line>
+                      <polyline points="10 9 9 9 8 9"></polyline>
+                    </svg>
+                    {ensureFileLoading ? 'Loading...' : 'View Ensure File'}
+                  </button>
+                  <button
+                    className="btn btn-secondary btn-small"
+                    onClick={() => setShowGraph(true)}
+                    title="View full dependency tree"
+                  >
+                    <svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" strokeWidth="2" style={{ marginRight: '6px' }}>
+                      <circle cx="12" cy="12" r="3"></circle>
+                      <circle cx="4" cy="4" r="2"></circle>
+                      <circle cx="20" cy="4" r="2"></circle>
+                      <circle cx="4" cy="20" r="2"></circle>
+                      <circle cx="20" cy="20" r="2"></circle>
+                      <line x1="9.5" y1="9.5" x2="5.5" y2="5.5"></line>
+                      <line x1="14.5" y1="9.5" x2="18.5" y2="5.5"></line>
+                      <line x1="9.5" y1="14.5" x2="5.5" y2="18.5"></line>
+                      <line x1="14.5" y1="14.5" x2="18.5" y2="18.5"></line>
+                    </svg>
+                    View Graph
+                  </button>
+                </>
+              )}
+            </div>
+          </div>
+          <div className="dependencies-tag-select">
+            {selectedTag && (
+              <select
+                className="tag-selector"
+                value={selectedTag.id}
+                onChange={(e) => {
+                  const tag = tags.find(t => t.id === e.target.value);
+                  if (tag) setSelectedTag(tag);
+                }}
+              >
+                {tags.map(t => (
+                  <option key={t.id} value={t.id}>
+                    {t.name}{t.version ? ` (${t.version})` : ''}
+                  </option>
+                ))}
+              </select>
+            )}
+          </div>
+
+          {depsLoading ? (
+            <div className="deps-loading">Loading dependencies...</div>
+          ) : depsError ? (
+            <div className="deps-error">{depsError}</div>
+          ) : dependencies.length === 0 ? (
+            <div className="deps-empty">
+              {selectedTag ? (
+                <span><strong>{selectedTag.name}</strong> has no dependencies</span>
+              ) : (
+                <span>No dependencies</span>
+              )}
+            </div>
+          ) : (
+            <div className="deps-list">
+              <div className="deps-summary">
+                <strong>{selectedTag?.name}</strong> has {dependencies.length} {dependencies.length === 1 ? 'dependency' : 'dependencies'}:
+              </div>
+              <ul className="deps-items">
+                {dependencies.map((dep) => (
+                  <li key={dep.id} className="dep-item">
+                    <Link
+                      to={`/project/${dep.project}/${dep.package}`}
+                      className="dep-link"
+                    >
+                      {dep.project}/{dep.package}
+                    </Link>
+                    <span className="dep-constraint">
+                      @ {dep.version || dep.tag}
+                    </span>
+                    <span className="dep-status dep-status--ok" title="Package exists">
+                      &#10003;
+                    </span>
+                  </li>
+                ))}
+              </ul>
+            </div>
+          )}
+        </div>
+      )}
+
+      {/* Used By (Reverse Dependencies) Section */}
+      <div className="used-by-section card">
+        <h3>Used By</h3>
+
+        {reverseDepsLoading ? (
+          <div className="deps-loading">Loading reverse dependencies...</div>
+        ) : reverseDepsError ? (
+          <div className="deps-error">{reverseDepsError}</div>
+        ) : reverseDeps.length === 0 ? (
+          <div className="deps-empty">No packages depend on this package</div>
+        ) : (
           <div className="reverse-deps-list">
             <div className="deps-summary">
               {reverseDepsTotal} {reverseDepsTotal === 1 ? 'package depends' : 'packages depend'} on this:
@@ -736,6 +734,78 @@ function PackagePage() {
               </div>
             )}
           </div>
+        )}
+      </div>
+
+      <div className="download-by-id-section card">
+        <h3>Download by Artifact ID</h3>
+        <div className="download-by-id-form">
+          <input
+            type="text"
+            value={artifactIdInput}
+            onChange={(e) => setArtifactIdInput(e.target.value.toLowerCase().replace(/[^a-f0-9]/g, '').slice(0, 64))}
+            placeholder="Enter SHA256 artifact ID (64 hex characters)"
+            className="artifact-id-input"
+          />
+          <a
+            href={artifactIdInput.length === 64 ? getDownloadUrl(projectName!, packageName!, `artifact:${artifactIdInput}`) : '#'}
+            className={`btn btn-primary ${artifactIdInput.length !== 64 ? 'btn-disabled' : ''}`}
+            download
+            onClick={(e) => {
+              if (artifactIdInput.length !== 64) {
+                e.preventDefault();
+              }
+            }}
+          >
+            Download
+          </a>
+        </div>
+        {artifactIdInput.length > 0 && artifactIdInput.length !== 64 && (
+          <p className="validation-hint">Artifact ID must be exactly 64 hex characters ({artifactIdInput.length}/64)</p>
+        )}
+      </div>
+
+      {user && canWrite && (
+        <div className="create-tag-section card">
+          <h3>Create / Update Tag</h3>
+          <p className="section-description">Point a tag at any existing artifact by its ID</p>
+          <form onSubmit={handleCreateTag} className="create-tag-form">
+            <div className="form-row">
+              <div className="form-group">
+                <label htmlFor="create-tag-name">Tag Name</label>
+                <input
+                  id="create-tag-name"
+                  type="text"
+                  value={createTagName}
+                  onChange={(e) => setCreateTagName(e.target.value)}
+                  placeholder="latest, stable, v1.0.0..."
+                  disabled={createTagLoading}
+                />
+              </div>
+              <div className="form-group form-group--wide">
+                <label htmlFor="create-tag-artifact">Artifact ID</label>
+                <input
+                  id="create-tag-artifact"
+                  type="text"
+                  value={createTagArtifactId}
+                  onChange={(e) => setCreateTagArtifactId(e.target.value.toLowerCase().replace(/[^a-f0-9]/g, '').slice(0, 64))}
+                  placeholder="SHA256 hash (64 hex characters)"
+                  className="artifact-id-input"
+                  disabled={createTagLoading}
+                />
+              </div>
+              <button
+                type="submit"
+                className="btn btn-primary"
+                disabled={createTagLoading || !createTagName.trim() || createTagArtifactId.length !== 64}
+              >
+                {createTagLoading ? 'Creating...' : 'Create Tag'}
+              </button>
+            </div>
+            {createTagArtifactId.length > 0 && createTagArtifactId.length !== 64 && (
+              <p className="validation-hint">Artifact ID must be exactly 64 hex characters ({createTagArtifactId.length}/64)</p>
+            )}
+          </form>
         </div>
       )}
 
@@ -761,118 +831,6 @@ function PackagePage() {
         />
       )}
 
-      {/* Upload Modal */}
-      {showUploadModal && (
-        <div className="modal-overlay" onClick={() => setShowUploadModal(false)}>
-          <div className="upload-modal" onClick={(e) => e.stopPropagation()}>
-            <div className="modal-header">
-              <h3>Upload Artifact</h3>
-              <button
-                className="modal-close"
-                onClick={() => setShowUploadModal(false)}
-                title="Close"
-              >
-                <svg width="20" height="20" viewBox="0 0 24 24" fill="none" stroke="currentColor" strokeWidth="2">
-                  <line x1="18" y1="6" x2="6" y2="18"></line>
-                  <line x1="6" y1="6" x2="18" y2="18"></line>
-                </svg>
-              </button>
-            </div>
-            <div className="modal-body">
-              <div className="form-group">
-                <label htmlFor="upload-tag">Tag (optional)</label>
-                <input
-                  id="upload-tag"
-                  type="text"
-                  value={uploadTag}
-                  onChange={(e) => setUploadTag(e.target.value)}
-                  placeholder="v1.0.0, latest, stable..."
-                />
-              </div>
-              <DragDropUpload
-                projectName={projectName!}
-                packageName={packageName!}
-                tag={uploadTag || undefined}
-                onUploadComplete={(result) => {
-                  handleUploadComplete(result);
-                  setShowUploadModal(false);
-                  setUploadTag('');
-                }}
-                onUploadError={handleUploadError}
-              />
-            </div>
-          </div>
-        </div>
-      )}
-
-      {/* Create/Update Tag Modal */}
-      {showCreateTagModal && (
-        <div className="modal-overlay" onClick={() => setShowCreateTagModal(false)}>
-          <div className="create-tag-modal" onClick={(e) => e.stopPropagation()}>
-            <div className="modal-header">
-              <h3>Create / Update Tag</h3>
-              <button
-                className="modal-close"
-                onClick={() => { setShowCreateTagModal(false); setCreateTagName(''); setCreateTagArtifactId(''); }}
-                title="Close"
-              >
-                <svg width="20" height="20" viewBox="0 0 24 24" fill="none" stroke="currentColor" strokeWidth="2">
-                  <line x1="18" y1="6" x2="6" y2="18"></line>
-                  <line x1="6" y1="6" x2="18" y2="18"></line>
-                </svg>
-              </button>
-            </div>
-            <div className="modal-body">
-              <p className="modal-description">Point a tag at an artifact by its ID</p>
-              <form onSubmit={(e) => { handleCreateTag(e); setShowCreateTagModal(false); }}>
-                <div className="form-group">
-                  <label htmlFor="modal-tag-name">Tag Name</label>
-                  <input
-                    id="modal-tag-name"
-                    type="text"
-                    value={createTagName}
-                    onChange={(e) => setCreateTagName(e.target.value)}
-                    placeholder="latest, stable, v1.0.0..."
-                    disabled={createTagLoading}
-                  />
-                </div>
-                <div className="form-group">
-                  <label htmlFor="modal-artifact-id">Artifact ID</label>
-                  <input
-                    id="modal-artifact-id"
-                    type="text"
-                    value={createTagArtifactId}
-                    onChange={(e) => setCreateTagArtifactId(e.target.value.toLowerCase().replace(/[^a-f0-9]/g, '').slice(0, 64))}
-                    placeholder="SHA256 hash (64 hex characters)"
-                    className="artifact-id-input"
-                    disabled={createTagLoading}
-                  />
-                  {createTagArtifactId.length > 0 && createTagArtifactId.length !== 64 && (
-                    <p className="validation-hint">{createTagArtifactId.length}/64 characters</p>
-                  )}
-                </div>
-                <div className="modal-actions">
-                  <button
-                    type="button"
-                    className="btn btn-secondary"
-                    onClick={() => { setShowCreateTagModal(false); setCreateTagName(''); setCreateTagArtifactId(''); }}
-                  >
-                    Cancel
-                  </button>
-                  <button
-                    type="submit"
-                    className="btn btn-primary"
-                    disabled={createTagLoading || !createTagName.trim() || createTagArtifactId.length !== 64}
-                  >
-                    {createTagLoading ? 'Creating...' : 'Create Tag'}
-                  </button>
-                </div>
-              </form>
-            </div>
-          </div>
-        </div>
-      )}
-
       {/* Ensure File Modal */}
       {showEnsureFile && (
         <div className="modal-overlay" onClick={() => setShowEnsureFile(false)}>
@@ -914,107 +872,6 @@ function PackagePage() {
           </div>
         </div>
       )}
-
-      {/* Dependencies Modal */}
-      {showDepsModal && selectedTag && (
-        <div className="modal-overlay" onClick={() => setShowDepsModal(false)}>
-          <div className="deps-modal" onClick={(e) => e.stopPropagation()}>
-            <div className="modal-header">
-              <h3>Dependencies for {selectedTag.version || selectedTag.name}</h3>
-              <button
-                className="modal-close"
-                onClick={() => setShowDepsModal(false)}
-                title="Close"
-              >
-                <svg width="20" height="20" viewBox="0 0 24 24" fill="none" stroke="currentColor" strokeWidth="2">
-                  <line x1="18" y1="6" x2="6" y2="18"></line>
-                  <line x1="6" y1="6" x2="18" y2="18"></line>
-                </svg>
-              </button>
-            </div>
-            <div className="modal-body">
-              <div className="deps-modal-controls">
-                <button
-                  className="btn btn-secondary btn-small"
-                  onClick={fetchEnsureFile}
-                  disabled={ensureFileLoading}
-                >
-                  View Ensure File
-                </button>
-                <button
-                  className="btn btn-secondary btn-small"
-                  onClick={() => { setShowDepsModal(false); setShowGraph(true); }}
-                >
-                  View Graph
-                </button>
-              </div>
-              {depsLoading ? (
-                <div className="deps-loading">Loading dependencies...</div>
-              ) : depsError ? (
-                <div className="deps-error">{depsError}</div>
-              ) : dependencies.length === 0 ? (
-                <div className="deps-empty">No dependencies</div>
-              ) : (
-                <div className="deps-list">
-                  <div className="deps-summary">
-                    {dependencies.length} {dependencies.length === 1 ? 'dependency' : 'dependencies'}:
-                  </div>
-                  <ul className="deps-items">
-                    {dependencies.map((dep) => (
-                      <li key={dep.id} className="dep-item">
-                        <Link
-                          to={`/project/${dep.project}/${dep.package}`}
-                          className="dep-link"
-                          onClick={() => setShowDepsModal(false)}
-                        >
-                          {dep.project}/{dep.package}
-                        </Link>
-                        <span className="dep-constraint">
-                          @ {dep.version || dep.tag}
-                        </span>
-                        <span className="dep-status dep-status--ok" title="Package exists">
-                          &#10003;
-                        </span>
-                      </li>
-                    ))}
-                  </ul>
-                </div>
-              )}
-            </div>
-          </div>
-        </div>
-      )}
-
-      {/* Artifact ID Modal */}
-      {showArtifactIdModal && viewArtifactId && (
-        <div className="modal-overlay" onClick={() => setShowArtifactIdModal(false)}>
-          <div className="artifact-id-modal" onClick={(e) => e.stopPropagation()}>
-            <div className="modal-header">
-              <h3>Artifact ID</h3>
-              <button
-                className="modal-close"
-                onClick={() => setShowArtifactIdModal(false)}
-                title="Close"
-              >
-                <svg width="20" height="20" viewBox="0 0 24 24" fill="none" stroke="currentColor" strokeWidth="2">
-                  <line x1="18" y1="6" x2="6" y2="18"></line>
-                  <line x1="6" y1="6" x2="18" y2="18"></line>
-                </svg>
-              </button>
-            </div>
-            <div className="modal-body">
-              <p className="modal-description">SHA256 hash identifying this artifact:</p>
-              <div className="artifact-id-display">
-                <code>{viewArtifactId}</code>
-                <CopyButton text={viewArtifactId} />
-              </div>
-            </div>
-          </div>
-        </div>
-      )}
-
-      {/* Action Menu Dropdown */}
-      {renderActionMenu()}
     </div>
   );
 }

frontend/src/pages/ProjectPage.tsx

@@ -214,7 +214,7 @@ function ProjectPage() {
           </div>
         </div>
         <div className="page-header__actions">
-          {canAdmin && !project.team_id && !project.is_system && (
+          {canAdmin && !project.team_id && (
             <button
               className="btn btn-secondary"
               onClick={() => navigate(`/project/${projectName}/settings`)}
@@ -227,11 +227,11 @@ function ProjectPage() {
               Settings
             </button>
           )}
-          {canWrite && !project.is_system ? (
+          {canWrite ? (
             <button className="btn btn-primary" onClick={() => setShowForm(!showForm)}>
               {showForm ? 'Cancel' : '+ New Package'}
             </button>
-          ) : user && !project.is_system ? (
+          ) : user ? (
             <span className="text-muted" title="You have read-only access to this project">
               Read-only access
             </span>
@@ -294,20 +294,18 @@ function ProjectPage() {
           placeholder="Filter packages..."
           className="list-controls__search"
         />
-        {!project?.is_system && (
-          <select
-            className="list-controls__select"
-            value={format}
-            onChange={(e) => handleFormatChange(e.target.value)}
-          >
-            <option value="">All formats</option>
-            {FORMAT_OPTIONS.map((f) => (
-              <option key={f} value={f}>
-                {f}
-              </option>
-            ))}
-          </select>
-        )}
+        <select
+          className="list-controls__select"
+          value={format}
+          onChange={(e) => handleFormatChange(e.target.value)}
+        >
+          <option value="">All formats</option>
+          {FORMAT_OPTIONS.map((f) => (
+            <option key={f} value={f}>
+              {f}
+            </option>
+          ))}
+        </select>
       </div>
 
       {hasActiveFilters && (
@@ -343,19 +341,19 @@ function ProjectPage() {
               className: 'cell-description',
               render: (pkg) => pkg.description || '—',
             },
-            ...(!project?.is_system ? [{
+            {
               key: 'format',
               header: 'Format',
-              render: (pkg: Package) => <Badge variant="default">{pkg.format}</Badge>,
-            }] : []),
-            ...(!project?.is_system ? [{
+              render: (pkg) => <Badge variant="default">{pkg.format}</Badge>,
+            },
+            {
               key: 'tag_count',
               header: 'Tags',
-              render: (pkg: Package) => pkg.tag_count ?? '—',
-            }] : []),
+              render: (pkg) => pkg.tag_count ?? '—',
+            },
             {
               key: 'artifact_count',
-              header: project?.is_system ? 'Versions' : 'Artifacts',
+              header: 'Artifacts',
               render: (pkg) => pkg.artifact_count ?? '—',
             },
             {
@@ -364,12 +362,12 @@ function ProjectPage() {
               render: (pkg) =>
                 pkg.total_size !== undefined && pkg.total_size > 0 ? formatBytes(pkg.total_size) : '—',
             },
-            ...(!project?.is_system ? [{
+            {
               key: 'latest_tag',
               header: 'Latest',
-              render: (pkg: Package) =>
+              render: (pkg) =>
                 pkg.latest_tag ? <strong style={{ color: 'var(--accent-primary)' }}>{pkg.latest_tag}</strong> : '—',
-            }] : []),
+            },
             {
               key: 'created_at',
               header: 'Created',

frontend/src/types.ts

@@ -433,13 +433,6 @@ export interface ResolvedArtifact {
   download_url: string;
 }
 
-export interface MissingDependency {
-  project: string;
-  package: string;
-  constraint: string | null;
-  required_by: string | null;
-}
-
 export interface DependencyResolutionResponse {
   requested: {
     project: string;
@@ -447,7 +440,6 @@ export interface DependencyResolutionResponse {
     ref: string;
   };
   resolved: ResolvedArtifact[];
-  missing: MissingDependency[];
   total_size: number;
   artifact_count: number;
 }
@@ -565,3 +557,15 @@ export interface UpstreamSourceTestResult {
   source_id: string;
   source_name: string;
 }
+
+// Cache Settings types
+export interface CacheSettings {
+  auto_create_system_projects: boolean;
+  auto_create_system_projects_env_override: boolean | null;
+  created_at: string | null;
+  updated_at: string | null;
+}
+
+export interface CacheSettingsUpdate {
+  auto_create_system_projects?: boolean;
+}

helm/orchard/templates/deployment.yaml

@@ -144,20 +144,6 @@ spec:
             - name: ORCHARD_DATABASE_POOL_TIMEOUT
               value: {{ .Values.orchard.database.poolTimeout | quote }}
             {{- end }}
-            {{- if .Values.orchard.pypiCache }}
-            {{- if .Values.orchard.pypiCache.workers }}
-            - name: ORCHARD_PYPI_CACHE_WORKERS
-              value: {{ .Values.orchard.pypiCache.workers | quote }}
-            {{- end }}
-            {{- if .Values.orchard.pypiCache.maxDepth }}
-            - name: ORCHARD_PYPI_CACHE_MAX_DEPTH
-              value: {{ .Values.orchard.pypiCache.maxDepth | quote }}
-            {{- end }}
-            {{- if .Values.orchard.pypiCache.maxAttempts }}
-            - name: ORCHARD_PYPI_CACHE_MAX_ATTEMPTS
-              value: {{ .Values.orchard.pypiCache.maxAttempts | quote }}
-            {{- end }}
-            {{- end }}
             {{- if .Values.orchard.auth }}
             {{- if or .Values.orchard.auth.secretsManager .Values.orchard.auth.existingSecret .Values.orchard.auth.adminPassword }}
             - name: ORCHARD_ADMIN_PASSWORD

helm/orchard/values-dev.yaml

@@ -59,10 +59,10 @@ ingress:
 resources:
   limits:
     cpu: 500m
-    memory: 1Gi
+    memory: 512Mi
   requests:
     cpu: 200m
-    memory: 1Gi
+    memory: 512Mi
 
 livenessProbe:
   httpGet:
@@ -124,12 +124,6 @@ orchard:
     mode: "presigned"
     presignedUrlExpiry: 3600
 
-  # PyPI Cache Worker settings (reduced workers to limit memory usage)
-  pypiCache:
-    workers: 1
-    maxDepth: 10
-    maxAttempts: 3
-
   # Relaxed rate limits for dev/feature environments (allows integration tests to run)
   rateLimit:
     login: "1000/minute"  # Default is 5/minute, relaxed for CI integration tests

helm/orchard/values-prod.yaml

@@ -57,10 +57,10 @@ ingress:
 resources:
   limits:
     cpu: 500m
-    memory: 768Mi
+    memory: 512Mi
   requests:
     cpu: 500m
-    memory: 768Mi
+    memory: 512Mi
 
 livenessProbe:
   httpGet:
@@ -121,12 +121,6 @@ orchard:
     mode: "presigned"
     presignedUrlExpiry: 3600
 
-  # PyPI Cache Worker settings (reduced workers to limit memory usage)
-  pypiCache:
-    workers: 2
-    maxDepth: 10
-    maxAttempts: 3
-
 # PostgreSQL subchart - disabled in prod, using RDS
 postgresql:
   enabled: false

helm/orchard/values-stage.yaml

@@ -56,10 +56,10 @@ ingress:
 resources:
   limits:
     cpu: 500m
-    memory: 768Mi
+    memory: 512Mi
   requests:
     cpu: 500m
-    memory: 768Mi
+    memory: 512Mi
 
 livenessProbe:
   httpGet:
@@ -122,12 +122,6 @@ orchard:
     mode: "presigned"  # presigned, redirect, or proxy
     presignedUrlExpiry: 3600  # Presigned URL expiry in seconds
 
-  # PyPI Cache Worker settings (reduced workers to limit memory usage)
-  pypiCache:
-    workers: 2
-    maxDepth: 10
-    maxAttempts: 3
-
   # Relaxed rate limits for stage (allows CI integration tests to run)
   rateLimit:
     login: "1000/minute"  # Default is 5/minute, relaxed for CI integration tests

helm/orchard/values.yaml

@@ -54,10 +54,10 @@ ingress:
 resources:
   limits:
     cpu: 500m
-    memory: 768Mi
+    memory: 512Mi
   requests:
     cpu: 500m
-    memory: 768Mi
+    memory: 512Mi
 
 livenessProbe:
   httpGet:
@@ -120,12 +120,6 @@ orchard:
     mode: "presigned"  # presigned, redirect, or proxy
     presignedUrlExpiry: 3600  # Presigned URL expiry in seconds
 
-  # PyPI Cache Worker settings
-  pypiCache:
-    workers: 2  # Number of concurrent cache workers (reduced to limit memory usage)
-    maxDepth: 10  # Maximum recursion depth for dependency caching
-    maxAttempts: 3  # Maximum retry attempts for failed cache tasks
-
   # Authentication settings
   auth:
     # Option 1: Plain admin password (creates K8s secret)

migrations/011_pypi_cache_tasks.sql

@@ -1,55 +0,0 @@
--- Migration: 011_pypi_cache_tasks
--- Description: Add table for tracking PyPI dependency caching tasks
--- Date: 2026-02-02
-
--- Table for tracking PyPI cache tasks with retry support
-CREATE TABLE pypi_cache_tasks (
-    id UUID PRIMARY KEY DEFAULT gen_random_uuid(),
-
-    -- What to cache
-    package_name VARCHAR(255) NOT NULL,
-    version_constraint VARCHAR(255),
-
-    -- Origin tracking
-    parent_task_id UUID REFERENCES pypi_cache_tasks(id) ON DELETE SET NULL,
-    depth INTEGER NOT NULL DEFAULT 0,
-    triggered_by_artifact VARCHAR(64) REFERENCES artifacts(id) ON DELETE SET NULL,
-
-    -- Status
-    status VARCHAR(20) NOT NULL DEFAULT 'pending',
-    attempts INTEGER NOT NULL DEFAULT 0,
-    max_attempts INTEGER NOT NULL DEFAULT 3,
-
-    -- Results
-    cached_artifact_id VARCHAR(64) REFERENCES artifacts(id) ON DELETE SET NULL,
-    error_message TEXT,
-
-    -- Timing
-    created_at TIMESTAMP WITH TIME ZONE NOT NULL DEFAULT NOW(),
-    started_at TIMESTAMP WITH TIME ZONE,
-    completed_at TIMESTAMP WITH TIME ZONE,
-    next_retry_at TIMESTAMP WITH TIME ZONE,
-
-    -- Constraints
-    CONSTRAINT check_task_status CHECK (status IN ('pending', 'in_progress', 'completed', 'failed')),
-    CONSTRAINT check_depth_non_negative CHECK (depth >= 0),
-    CONSTRAINT check_attempts_non_negative CHECK (attempts >= 0)
-);
-
--- Index for finding tasks ready to process (pending with retry time passed)
-CREATE INDEX idx_pypi_cache_tasks_status_retry ON pypi_cache_tasks(status, next_retry_at);
-
--- Index for deduplication check (is this package already queued?)
-CREATE INDEX idx_pypi_cache_tasks_package_status ON pypi_cache_tasks(package_name, status);
-
--- Index for tracing dependency chains
-CREATE INDEX idx_pypi_cache_tasks_parent ON pypi_cache_tasks(parent_task_id);
-
--- Index for finding tasks by artifact that triggered them
-CREATE INDEX idx_pypi_cache_tasks_triggered_by ON pypi_cache_tasks(triggered_by_artifact);
-
--- Index for finding tasks by cached artifact
-CREATE INDEX idx_pypi_cache_tasks_cached_artifact ON pypi_cache_tasks(cached_artifact_id);
-
--- Index for sorting by depth and creation time (processing order)
-CREATE INDEX idx_pypi_cache_tasks_depth_created ON pypi_cache_tasks(depth, created_at);