codegraphcontext 0.4.18__py3-none-any.whl → 0.5.1__py3-none-any.whl

codegraphcontext/api/app.py

@@ -17,7 +17,10 @@ def create_app() -> FastAPI:
     app.add_middleware(
         CORSMiddleware,
         allow_origins=["*"], # In production, restrict this
-        allow_credentials=True,
+        # Credentials must stay disabled while origins is a wildcard; the
+        # combination is rejected by browsers and would leak cookie-authed
+        # responses to any site.
+        allow_credentials=False,
         allow_methods=["*"],
         allow_headers=["*"],
     )

codegraphcontext/api/mcp_sse.py

@@ -8,16 +8,17 @@ from mcp.types import Tool, TextContent, ServerCapabilities, ToolsCapability
 from mcp.server.sse import SseServerTransport
 
 from codegraphcontext.api.router import get_server
-from codegraphcontext.tool_definitions import TOOLS
+from codegraphcontext.server import _strip_workspace_prefix, _apply_response_token_limit
 
 # Create the MCP Server instance using the SDK
 mcp_server = Server("CodeGraphContext")
 
 @mcp_server.list_tools()
 async def handle_list_tools() -> list[Tool]:
-    """List available tools."""
+    """List available tools (honors disabledTools from mcp.json)."""
+    server = get_server()
     tools = []
-    for name, defn in TOOLS.items():
+    for name, defn in server.tools.items():
         tools.append(Tool(
             name=name,
             description=defn["description"],
@@ -33,12 +34,16 @@ async def handle_call_tool(name: str, arguments: dict | None) -> list[TextConten
     
     # Execute via the existing handler logic
     result = await server.handle_tool_call(name, args)
+    result = _strip_workspace_prefix(result)
     
     if "error" in result:
         return [TextContent(type="text", text=f"Error: {result['error']}")]
     
-    # Format result as JSON string for the AI
-    return [TextContent(type="text", text=json.dumps(result, indent=2))]
+    # Format result as JSON string for the AI, with the same token budget
+    # the stdio transport applies.
+    response_text = json.dumps(result, indent=2)
+    response_text = _apply_response_token_limit(name, response_text)
+    return [TextContent(type="text", text=response_text)]
 
 # Create the SSE transport. 
 # The messages_url is where the client will POST JSON-RPC messages.

codegraphcontext/api/router.py

@@ -91,12 +91,9 @@ async def index_repository(
     background_tasks: BackgroundTasks,
     server: MCPServer = Depends(get_server)
 ):
-    args = {
-        "path": request.path,
-        "repo_name": request.repo_name,
-        "branch": request.branch,
-        "force": request.force
-    }
+    # The add_code_to_graph handler only understands "path" (and is_dependency);
+    # repo_name/branch/force from the request model are not supported by it.
+    args = {"path": request.path}
 
     try:
         result = await server.handle_tool_call(

codegraphcontext/cli/cli_helpers.py

@@ -35,6 +35,7 @@ from .config_manager import (
     register_repo_in_context,
     ensure_first_run_bootstrap,
     ContextNotFoundError,
+    is_db_deletion_allowed,
 )
 
 console = Console()
@@ -673,14 +674,32 @@ def reindex_helper(path: str, context: Optional[str] = None):
         db_manager.close_driver()
 
 
-def update_helper(path: str, context: Optional[str] = None):
-    """Update/refresh index for a path (alias for reindex)."""
+def update_helper(path: str, context: Optional[str] = None, quiet: bool = False):
+    """Update/refresh index for a path (alias for reindex).
+
+    When *quiet* is True (e.g. when invoked from Git hooks with --quiet),
+    Rich console output, including progress rendering, is suppressed.
+    """
+    if quiet:
+        console.quiet = True
+        try:
+            reindex_helper(path, context)
+        finally:
+            console.quiet = False
+        return
     console.print("[cyan]Updating repository index...[/cyan]")
     reindex_helper(path, context)
 
 
 def clean_helper(context: Optional[str] = None):
     """Remove orphaned nodes and relationships from the database."""
+    if not is_db_deletion_allowed():
+        console.print(
+            "[bold red]Error:[/bold red] Database cleanup is disabled. "
+            "Set ALLOW_DB_DELETION=true in config to enable."
+        )
+        raise typer.Exit(code=1)
+
     services = _initialize_services(context)
     if not all(services[:3]):
         _fail_services_init()
@@ -738,6 +757,9 @@ def stats_helper(path: str = None, context: Optional[str] = None):
         if path:
             # Stats for specific repository
             path_obj = Path(path).resolve()
+            # Paths are stored with forward slashes (as_posix) in the graph DB,
+            # so lookups must use the same normalization on Windows too.
+            repo_path_str = path_obj.as_posix()
             console.print(f"[cyan]📊 Statistics for: {path_obj}[/cyan]\n")
             
             with db_manager.get_driver().session() as session:
@@ -746,7 +768,7 @@ def stats_helper(path: str = None, context: Optional[str] = None):
                 MATCH (r:Repository {path: $path})
                 RETURN r
                 """
-                result = session.run(repo_query, path=str(path_obj))
+                result = session.run(repo_query, path=repo_path_str)
                 if not result.single():
                     console.print(f"[red]Repository not found: {path_obj}[/red]")
                     return
@@ -755,20 +777,20 @@ def stats_helper(path: str = None, context: Optional[str] = None):
                 # Get stats using separate queries to handle depth and avoid Cartesian products
                 # 1. Files
                 file_query = "MATCH (r:Repository {path: $path})-[:CONTAINS*]->(f:File) RETURN count(f) as c"
-                file_count = session.run(file_query, path=str(path_obj)).single()["c"]
+                file_count = session.run(file_query, path=repo_path_str).single()["c"]
                 
                 # 2. Functions (including methods in classes)
                 func_query = "MATCH (r:Repository {path: $path})-[:CONTAINS*]->(func:Function) RETURN count(func) as c"
-                func_count = session.run(func_query, path=str(path_obj)).single()["c"]
+                func_count = session.run(func_query, path=repo_path_str).single()["c"]
                 
                 # 3. Classes
                 class_query = "MATCH (r:Repository {path: $path})-[:CONTAINS*]->(c:Class) RETURN count(c) as c"
-                class_count = session.run(class_query, path=str(path_obj)).single()["c"]
+                class_count = session.run(class_query, path=repo_path_str).single()["c"]
                 
                 # 4. Modules (imported) - Note: Module nodes are outside the repo structure usually, connected via IMPORTS
                 # We need to traverse from files to modules
                 module_query = "MATCH (r:Repository {path: $path})-[:CONTAINS*]->(f:File)-[:IMPORTS]->(m:Module) RETURN count(DISTINCT m) as c"
-                module_count = session.run(module_query, path=str(path_obj)).single()["c"]
+                module_count = session.run(module_query, path=repo_path_str).single()["c"]
 
                 table = Table(show_header=True, header_style="bold magenta")
                 table.add_column("Metric", style="cyan")
@@ -869,7 +891,7 @@ def watch_helper(path: str, context: Optional[str] = None, use_polling: Optional
             with code_finder.driver.session() as _s:
                 _r = _s.run(
                     "MATCH (n:File) WHERE n.path STARTS WITH $p RETURN count(n) AS c",
-                    p=str(path_obj) + "/"
+                    p=path_obj.as_posix() + "/"
                 )
                 _count = _r.single()["c"]
             if _count > 100:

codegraphcontext/cli/config_manager.py

@@ -15,6 +15,19 @@ import yaml
 
 console = Console()
 
+
+def _atomic_write_text(path: Path, content: str, *, secure: bool = False) -> None:
+    """Write *content* to *path* atomically (temp file + replace)."""
+    path.parent.mkdir(parents=True, exist_ok=True)
+    tmp_path = path.with_suffix(path.suffix + ".tmp")
+    with open(tmp_path, "w", encoding="utf-8") as f:
+        f.write(content)
+        f.flush()
+        os.fsync(f.fileno())
+    os.replace(tmp_path, path)
+    if secure:
+        os.chmod(path, 0o600)
+
 # Configuration file location
 CONFIG_DIR = Path.home() / ".codegraphcontext"
 CONFIG_FILE = CONFIG_DIR / ".env"
@@ -385,30 +398,27 @@ def save_config(config: Dict[str, str], preserve_db_credentials: bool = True):
                 credentials_to_write[key] = config[key]
     
     try:
-        with open(CONFIG_FILE, "w", encoding="utf-8") as f:
-            f.write("# CodeGraphContext Configuration\n")
-            f.write(f"# Location: {CONFIG_FILE}\n\n")
-            
-            # Write database credentials first if they exist
-            if credentials_to_write:
-                f.write("# ===== Database Credentials =====\n")
-                for key in sorted(DATABASE_CREDENTIAL_KEYS):
-                    if key in credentials_to_write:
-                        f.write(f"{key}={credentials_to_write[key]}\n")
-                f.write("\n")
-            
-            # Write configuration settings
-            f.write("# ===== Configuration Settings =====\n")
-            for key, value in sorted(config.items()):
-                # Skip database credentials (already written above)
-                if key in DATABASE_CREDENTIAL_KEYS:
-                    continue
-                    
-                description = CONFIG_DESCRIPTIONS.get(key, "")
-                if description:
-                    f.write(f"# {description}\n")
-                f.write(f"{key}={value}\n\n")
-        
+        lines = [
+            "# CodeGraphContext Configuration",
+            f"# Location: {CONFIG_FILE}",
+            "",
+        ]
+        if credentials_to_write:
+            lines.append("# ===== Database Credentials =====")
+            for key in sorted(DATABASE_CREDENTIAL_KEYS):
+                if key in credentials_to_write:
+                    lines.append(f"{key}={credentials_to_write[key]}")
+            lines.append("")
+        lines.append("# ===== Configuration Settings =====")
+        for key, value in sorted(config.items()):
+            if key in DATABASE_CREDENTIAL_KEYS:
+                continue
+            description = CONFIG_DESCRIPTIONS.get(key, "")
+            if description:
+                lines.append(f"# {description}")
+            lines.append(f"{key}={value}")
+            lines.append("")
+        _atomic_write_text(CONFIG_FILE, "\n".join(lines), secure=True)
         console.print(f"[green]✅ Configuration saved to {CONFIG_FILE}[/green]")
     except Exception as e:
         console.print(f"[red]Error saving config: {e}[/red]")
@@ -804,8 +814,10 @@ def save_context_config(cfg: ContextConfig) -> None:
     }
 
     try:
-        with open(CONTEXT_CONFIG_FILE, "w", encoding="utf-8") as f:
-            yaml.dump(raw, f, default_flow_style=False, sort_keys=False)
+        _atomic_write_text(
+            CONTEXT_CONFIG_FILE,
+            yaml.dump(raw, default_flow_style=False, sort_keys=False),
+        )
     except Exception as e:
         console.print(f"[red]Error saving config.yaml: {e}[/red]")
 
@@ -887,10 +899,15 @@ def resolve_context(
 
         inherited_db = load_config().get("DEFAULT_DATABASE", "falkordb")
 
-        # Copy global .env into local context for easy per-repo tweaking
+        # Copy global .env into local context for easy per-repo tweaking.
+        # Guard against the self-copy case: when cwd is the home directory,
+        # local_cgc resolves to CONFIG_DIR itself, so `local_cgc / ".env"` is
+        # CONFIG_FILE. Copying a file onto itself raises shutil.SameFileError,
+        # which crashes resolve_context for any session started from home.
         import shutil
-        if CONFIG_FILE.exists():
-            shutil.copy2(CONFIG_FILE, local_cgc / ".env")
+        _target_env = local_cgc / ".env"
+        if CONFIG_FILE.exists() and _target_env.resolve() != CONFIG_FILE.resolve():
+            shutil.copy2(CONFIG_FILE, _target_env)
 
         local_yaml = local_cgc / "config.yaml"
         if not local_yaml.exists():
@@ -1172,8 +1189,10 @@ def _save_workspace_mappings(mappings: Dict[str, Dict[str, str]]) -> None:
             raw = {}
     raw["workspace_mappings"] = mappings
     try:
-        with open(CONTEXT_CONFIG_FILE, "w", encoding="utf-8") as f:
-            yaml.dump(raw, f, default_flow_style=False, sort_keys=False)
+        _atomic_write_text(
+            CONTEXT_CONFIG_FILE,
+            yaml.dump(raw, default_flow_style=False, sort_keys=False),
+        )
     except Exception as e:
         console.print(f"[red]Error saving workspace mappings: {e}[/red]")
 

codegraphcontext/cli/hook_manager.py

@@ -73,7 +73,7 @@ def install_hooks(start: Path | str | None = None, *, force: bool = False) -> Ho
             )
         hook_path.write_text(script, encoding="utf-8")
         mode = hook_path.stat().st_mode
-        hook_path.chmod(mode | stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH)
+        hook_path.chmod(mode | stat.S_IXUSR | stat.S_IXGRP)
 
     _ensure_gitattributes(repo.root)
     _configure_merge_driver(repo.root)

codegraphcontext/cli/main.py

@@ -85,8 +85,9 @@ app = typer.Typer(
 )
 console = Console(stderr=True)
 
-# Configure basic logging for the application.
-logging.basicConfig(level=logging.DEBUG, format='%(asctime)s - %(levelname)s - %(name)s - %(message)s')
+# Configure basic logging for the application. Default to WARNING so CLI
+# output stays clean; the root --debug flag switches this to DEBUG.
+logging.basicConfig(level=logging.WARNING, format='%(asctime)s - %(levelname)s - %(name)s - %(message)s')
 
 
 def get_version() -> str:
@@ -142,6 +143,7 @@ def mcp_start():
         # This typically happens if credentials are still not found after all checks.
         console.print(f"[bold red]Configuration Error:[/bold red] {e}")
         console.print("Please run `cgc neo4j setup` or use FalkorDB (default).")
+        raise typer.Exit(code=1) from e
     except KeyboardInterrupt:
         # Handle graceful shutdown on Ctrl+C.
         console.print("\n[bold yellow]Server stopped by user.[/bold yellow]")
@@ -177,8 +179,10 @@ def mcp_tools():
     except ValueError as e:
         console.print(f"[bold red]Error loading tools:[/bold red] {e}")
         console.print("Please ensure your database is configured correctly.")
+        raise typer.Exit(code=1) from e
     except Exception as e:
         console.print(f"[bold red]An unexpected error occurred:[/bold red] {e}")
+        raise typer.Exit(code=1) from e
 
 # Abbreviation for mcp setup
 @app.command("m", rich_help_panel="Shortcuts")
@@ -391,7 +395,6 @@ def _load_credentials(cli_context_flag: Optional[str] = None):
     # IMPORTANT: DB-selection keys set in the shell must win over .env defaults.
     # E.g. `DEFAULT_DATABASE=falkordb cgc index …` must not be overridden by
     # DEFAULT_DATABASE=neo4j sitting in ~/.codegraphcontext/.env
-    DB_OVERRIDE_KEYS = {"CGC_RUNTIME_DB_TYPE", "DEFAULT_DATABASE"}
     for key, value in merged_config.items():
         if value is not None:  # Only set non-None values
             if key in runtime_env:
@@ -627,7 +630,7 @@ def bundle_export(
     
     services = _initialize_services(context)
     if not all(services[:3]):
-        return
+        raise typer.Exit(code=1)
     db_manager, _, code_finder = services[:3]
     
     try:
@@ -697,7 +700,7 @@ def bundle_import(
     
     services = _initialize_services(context)
     if not all(services[:3]):
-        return
+        raise typer.Exit(code=1)
     db_manager, graph_builder, code_finder = services[:3]
     
     try:
@@ -790,6 +793,53 @@ def bundle_load(
         console.print("[dim]Use 'cgc registry list' to see available bundles[/dim]")
         raise typer.Exit(code=1)
 
+@bundle_app.command("merge")
+def bundle_merge(
+    ancestor: str = typer.Argument(..., help="Common ancestor version of the bundle (%O)"),
+    current: str = typer.Argument(..., help="Current branch version of the bundle (%A); also the merge result"),
+    other: str = typer.Argument(..., help="Other branch version of the bundle (%B)"),
+):
+    """
+    Git merge driver for .cgc bundle files.
+
+    Registered by `cgc hook install` as `merge.cgc-bundle.driver = cgc bundle
+    merge %O %A %B`. Git invokes it with temp files holding the ancestor (%O),
+    current (%A) and other (%B) versions; the merge result must be left in the
+    %A file and the driver must exit 0 for the merge to proceed.
+
+    Bundles are binary snapshots that cannot be merged line-by-line, so the
+    strategy is: if both sides are identical, accept either; otherwise keep
+    the current branch's version (already in the %A file) and warn that the
+    bundle should be regenerated with `cgc export` after the merge.
+    """
+    current_path = Path(current)
+    other_path = Path(other)
+
+    def _read_bytes(p: Path) -> bytes:
+        # A missing or empty temp file means the side has no content
+        # (e.g. the bundle is a new file on both branches → empty ancestor).
+        try:
+            return p.read_bytes() if p.exists() else b""
+        except OSError:
+            return b""
+
+    current_bytes = _read_bytes(current_path)
+    other_bytes = _read_bytes(other_path)
+
+    if current_bytes == other_bytes:
+        # Both branches have identical bundle contents; nothing to do.
+        raise typer.Exit(code=0)
+
+    # Keep the current branch's version (the %A file already contains it).
+    console.print(
+        "[yellow]⚠ Conflicting changes to a .cgc bundle were detected during merge. "
+        "Keeping the current branch's version.[/yellow]"
+    )
+    console.print(
+        "[yellow]The bundle may be stale — regenerate it with 'cgc export' after the merge.[/yellow]"
+    )
+    raise typer.Exit(code=0)
+
 # ============================================================================
 # HOOK COMMAND GROUP - Git integration
 # ============================================================================
@@ -1146,11 +1196,18 @@ def doctor():
                         all_checks_passed = False
         elif default_db == "falkordb":
             try:
-                import falkordblite  # noqa: F401
-                console.print("   [green]✓[/green] FalkorDB Lite is installed")
+                from codegraphcontext.core import is_falkordb_usable
+
+                if is_falkordb_usable():
+                    console.print("   [green]✓[/green] FalkorDB Lite is installed")
+                else:
+                    raise ImportError("FalkorDB Lite is not available on this platform")
             except ImportError:
-                console.print("   [yellow]⚠[/yellow] FalkorDB Lite not installed (Python 3.12+ only)")
+                # falkordb is the configured/default backend, so a missing
+                # FalkorDB Lite means the database cannot work — fail the check.
+                console.print("   [red]✗[/red] FalkorDB Lite not installed (Python 3.12+ only)")
                 console.print("       Run: pip install falkordblite")
+                all_checks_passed = False
         else:
             console.print(f"   [yellow]⚠[/yellow] No connectivity probe for backend '{default_db}'")
     except Exception as e:
@@ -1275,7 +1332,7 @@ def update(
     _load_credentials()
     if path is None:
         path = str(Path.cwd())
-    update_helper(path, context)
+    update_helper(path, context, quiet=quiet)
 
 @app.command()
 def clean(
@@ -1344,7 +1401,7 @@ def delete(
         # Delete all repositories
         services = _initialize_services(context)
         if not all(services[:3]):
-            return
+            raise typer.Exit(code=1)
         db_manager, graph_builder, code_finder = services[:3]
         
         try:
@@ -1409,7 +1466,14 @@ def delete(
             console.print("[red]Error: Please provide a path or use --all to delete all repositories[/red]")
             console.print("Usage: cgc delete <path> or cgc delete --all")
             raise typer.Exit(code=1)
-        
+
+        if not config_manager.is_db_deletion_allowed():
+            console.print(
+                "[bold red]Error:[/bold red] Repository deletion is disabled. "
+                "Set ALLOW_DB_DELETION=true in config to enable."
+            )
+            raise typer.Exit(code=1)
+
         delete_helper(path, context)
 
 
@@ -1593,7 +1657,7 @@ def find_by_name(
     _load_credentials()
     services = _initialize_services(context)
     if not all(services[:3]):
-        return
+        raise typer.Exit(code=1)
     db_manager, graph_builder, code_finder = services[:3]
 
     # Resolve effective fuzzy setting: CLI flag wins, else config, else true.
@@ -1725,7 +1789,7 @@ def find_by_pattern(
     _load_credentials()
     services = _initialize_services(context)
     if not all(services[:3]):
-        return
+        raise typer.Exit(code=1)
     db_manager, graph_builder, code_finder = services[:3]
     
     try:
@@ -1818,7 +1882,7 @@ def find_by_type(
     _load_credentials()
     services = _initialize_services(context)
     if not all(services[:3]):
-        return
+        raise typer.Exit(code=1)
     db_manager, graph_builder, code_finder = services[:3]
     
     try:
@@ -1873,7 +1937,7 @@ def find_by_variable(
     _load_credentials()
     services = _initialize_services(context)
     if not all(services[:3]):
-        return
+        raise typer.Exit(code=1)
     db_manager, graph_builder, code_finder = services[:3]
     
     try:
@@ -1919,7 +1983,7 @@ def find_by_content_search(
     _load_credentials()
     services = _initialize_services(context)
     if not all(services[:3]):
-        return
+        raise typer.Exit(code=1)
     db_manager, graph_builder, code_finder = services[:3]
     
     try:
@@ -1978,7 +2042,7 @@ def find_by_decorator_search(
     _load_credentials()
     services = _initialize_services(context)
     if not all(services[:3]):
-        return
+        raise typer.Exit(code=1)
     db_manager, graph_builder, code_finder = services[:3]
     
     try:
@@ -2026,7 +2090,7 @@ def find_by_argument_search(
     _load_credentials()
     services = _initialize_services(context)
     if not all(services[:3]):
-        return
+        raise typer.Exit(code=1)
     db_manager, graph_builder, code_finder = services[:3]
     
     try:
@@ -2082,7 +2146,7 @@ def analyze_calls(
     _load_credentials()
     services = _initialize_services(context)
     if not all(services[:3]):
-        return
+        raise typer.Exit(code=1)
     db_manager, graph_builder, code_finder = services[:3]
     
     try:
@@ -2138,7 +2202,7 @@ def analyze_callers(
     _load_credentials()
     services = _initialize_services(context)
     if not all(services[:3]):
-        return
+        raise typer.Exit(code=1)
     db_manager, graph_builder, code_finder = services[:3]
     
     try:
@@ -2199,7 +2263,7 @@ def analyze_chain(
     _load_credentials()
     services = _initialize_services(context)
     if not all(services[:3]):
-        return
+        raise typer.Exit(code=1)
     db_manager, graph_builder, code_finder = services[:3]
     
     try:
@@ -2269,7 +2333,7 @@ def analyze_kotlin_call_audit(
     _load_credentials()
     services = _initialize_services(context)
     if not all(services[:3]):
-        return
+        raise typer.Exit(code=1)
     db_manager, _, code_finder = services[:3]
 
     try:
@@ -2329,7 +2393,7 @@ def analyze_dependencies(
     _load_credentials()
     services = _initialize_services(context)
     if not all(services[:3]):
-        return
+        raise typer.Exit(code=1)
     db_manager, graph_builder, code_finder = services[:3]
     
     try:
@@ -2394,7 +2458,7 @@ def analyze_inheritance_tree(
     _load_credentials()
     services = _initialize_services(context)
     if not all(services[:3]):
-        return
+        raise typer.Exit(code=1)
     db_manager, graph_builder, code_finder = services[:3]
     
     try:
@@ -2464,7 +2528,7 @@ def analyze_complexity(
     _load_credentials()
     services = _initialize_services(context)
     if not all(services[:3]):
-        return
+        raise typer.Exit(code=1)
     db_manager, graph_builder, code_finder = services[:3]
 
     _FILE_EXTENSIONS = ('.py', '.js', '.ts', '.jsx', '.tsx', '.go', '.rs', '.rb',
@@ -2541,7 +2605,7 @@ def analyze_dead_code(
     _load_credentials()
     services = _initialize_services(context)
     if not all(services[:3]):
-        return
+        raise typer.Exit(code=1)
     db_manager, graph_builder, code_finder = services[:3]
     
     try:
@@ -2595,7 +2659,7 @@ def analyze_overrides(
     _load_credentials()
     services = _initialize_services(context)
     if not all(services[:3]):
-        return
+        raise typer.Exit(code=1)
     db_manager, graph_builder, code_finder = services[:3]
     
     try:
@@ -2650,7 +2714,7 @@ def analyze_variable_usage(
     _load_credentials()
     services = _initialize_services(context)
     if not all(services[:3]):
-        return
+        raise typer.Exit(code=1)
     db_manager, graph_builder, code_finder = services[:3]
     
     try:
@@ -2854,9 +2918,6 @@ def main(
         os.environ["CGC_RUNTIME_DB_TYPE"] = database
     # Initialize context object for sharing state with subcommands
     ctx.ensure_object(dict)
-    
-    if database:
-        os.environ["CGC_RUNTIME_DB_TYPE"] = database
 
     # Store visual flag in context for subcommands to access
     if visual:

codegraphcontext/cli/registry_commands.py

@@ -289,9 +289,16 @@ def download_bundle(name: str, output_dir: Optional[str] = None, auto_load: bool
             if auto_load:
                 console.print("[cyan]Using existing bundle for loading...[/cyan]")
                 return str(output_path)
-            return
+            return False
         output_path.unlink()
-    
+
+    from ..utils.path_sandbox import is_safe_download_url
+
+    if not is_safe_download_url(download_url):
+        console.print("[bold red]Refusing to download from untrusted URL.[/bold red]")
+        console.print("[dim]Only HTTPS downloads from approved hosts are allowed.[/dim]")
+        raise typer.Exit(code=1)
+
     # Download with progress bar
     try:
         console.print(f"[cyan]Downloading {clean_filename}...[/cyan]")
@@ -435,8 +442,8 @@ def load_bundle_command(bundle_name: str, clear_existing: bool = False):
                             stats["nodes"] = int(part.split(":")[1].strip().replace(",", ""))
                         elif "Edges:" in part:
                             stats["edges"] = int(part.split(":")[1].strip().replace(",", ""))
-                except:
-                    pass
+                except Exception as parse_exc:
+                    console.print(f"[dim]Could not parse bundle stats from message: {parse_exc}[/dim]")
             
             return (True, message, stats)
         else:

codegraphcontext/cli/setup_macos.py

@@ -16,12 +16,17 @@ def _brew_install_neo4j(run_command, console) -> str:
 def _brew_start(service: str, run_command, console) -> bool:
     return run_command(["brew", "services", "start", service], console, check=False) is not None
 
+def _escape_cypher_password(password: str) -> str:
+    return password.replace("\\", "\\\\").replace("'", "\\'")
+
+
 def _set_initial_password(new_pw: str, run_command, console) -> bool:
+    escaped_pw = _escape_cypher_password(new_pw)
     cmd = [
         "cypher-shell",
         "-u", "neo4j",
         "-p", "neo4j",
-        f"ALTER CURRENT USER SET PASSWORD FROM 'neo4j' TO '{new_pw}'",
+        f"ALTER CURRENT USER SET PASSWORD FROM 'neo4j' TO '{escaped_pw}'",
     ]
     return run_command(cmd, console, check=False) is not None