MCP fixes from staging e2e, clip hard-link fix

go.mod

@@ -17,7 +17,7 @@ require (
 	github.com/aws/aws-sdk-go-v2/service/ec2 v1.316.1
 	github.com/aws/aws-sdk-go-v2/service/ecr v1.27.0
 	github.com/aws/aws-sdk-go-v2/service/s3 v1.75.3
-	github.com/beam-cloud/clip v0.0.0-20260907023706-9420edd6f9ec
+	github.com/beam-cloud/clip v0.0.0-20260923215631-1c772eb678a5
 	github.com/beam-cloud/go-runc v0.0.0-20250911154456-bb45084abfe1
 	github.com/beam-cloud/goproc v0.1.12
 	github.com/beam-cloud/redislock v0.0.0-20250201162619-1b534b3be324
@@ -59,6 +59,7 @@ require (
 	github.com/redis/go-redis/v9 v9.5.1
 	github.com/rs/zerolog v1.34.0
 	github.com/s2-streamstore/s2-sdk-go v0.18.0
+	github.com/santhosh-tekuri/jsonschema/v6 v6.0.2
 	github.com/sashabaranov/go-openai v1.35.7
 	github.com/shirou/gopsutil/v4 v4.26.5
 	github.com/sirupsen/logrus v1.9.4
@@ -152,7 +153,6 @@ require (
 	github.com/pires/go-proxyproto v0.8.1 // indirect
 	github.com/planetscale/vtprotobuf v0.6.1-0.20240319094008-0393e58bdf10 // indirect
 	github.com/prometheus-community/pro-bing v0.4.0 // indirect
-	github.com/santhosh-tekuri/jsonschema/v6 v6.0.2 // indirect
 	github.com/satori/go.uuid v1.2.1-0.20181028125025-b2ce2384e17b // indirect
 	github.com/spiffe/go-spiffe/v2 v2.6.0 // indirect
 	github.com/stretchr/objx v0.5.2 // indirect

go.sum

@@ -161,8 +161,8 @@ github.com/aws/smithy-go v1.27.3/go.mod h1:YE2RhdIuDbA5E5bTdciG9KrW3+TiEONeUWCqx
 github.com/axiomhq/hyperloglog v0.0.0-20240319100328-84253e514e02 h1:bXAPYSbdYbS5VTy92NIUbeDI1qyggi+JYh5op9IFlcQ=
 github.com/axiomhq/hyperloglog v0.0.0-20240319100328-84253e514e02/go.mod h1:k08r+Yj1PRAmuayFiRK6MYuR5Ve4IuZtTfxErMIh0+c=
 github.com/aybabtme/rgbterm v0.0.0-20170906152045-cc83f3b3ce59/go.mod h1:q/89r3U2H7sSsE2t6Kca0lfwTK8JdoNGS/yzM/4iH5I=
-github.com/beam-cloud/clip v0.0.0-20260907023706-9420edd6f9ec h1:zcr7+ud507kcRJBHotXr4hcUzEoqfPEgjtcMW6eCZwo=
-github.com/beam-cloud/clip v0.0.0-20260907023706-9420edd6f9ec/go.mod h1:uymwDNMk1qoxElmDSlPzwYqZDriHDnW5VVyfK3YNuz8=
+github.com/beam-cloud/clip v0.0.0-20260923215631-1c772eb678a5 h1:OCIWtQpT3F+1PHcC5KOaOb+QEw2SkUo9Sh1lygsPPpM=
+github.com/beam-cloud/clip v0.0.0-20260923215631-1c772eb678a5/go.mod h1:uymwDNMk1qoxElmDSlPzwYqZDriHDnW5VVyfK3YNuz8=
 github.com/beam-cloud/geesefs v0.0.0-20260908033220-4484605feb60 h1:fX/Z5XOjVKYsWJO/FIOyCdWgg038BNHEpvp6lsiH49g=
 github.com/beam-cloud/geesefs v0.0.0-20260908033220-4484605feb60/go.mod h1:q0qGsu0wiOzf/5m9JGLqZ7WteYDaaLGgBwNmstb3og0=
 github.com/beam-cloud/geesefs/s3ext v0.0.0-20250606164905-2f3593d03f4f h1:XzHOu+erxeBO6D3fKVbd5DAlipl+PYZ3u+Ywb8m7Ovk=

pkg/api/v1/mcp_tools.go

@@ -8,6 +8,7 @@ import (
 	"encoding/json"
 	"errors"
 	"fmt"
+	"net/http"
 	"regexp"
 	"sort"
 	"strings"
@@ -212,9 +213,14 @@ func (g *MCPGroup) deleteApp(ctx context.Context, a *auth.AuthInfo, args toolArg
 	if err != nil {
 		return nil, err
 	}
-	if err := g.backendRepo.DeleteApp(ctx, app.ExternalId); err != nil {
+	// The REST handler stops deployments and containers before removing the record.
+	res, err := g.serve(ctx, http.MethodDelete, g.config.GatewayService.HTTP.GetExternalURL()+HttpServerBaseRoute+"/app/"+a.Workspace.ExternalId+"/"+app.ExternalId, nil, nil)
+	if err != nil {
 		return nil, err
 	}
+	if status := res.(map[string]any)["status"].(int); status >= 300 {
+		return nil, fmt.Errorf("delete app: HTTP %d", status)
+	}
 	return map[string]any{"deleted": app.Name, "app_id": app.ExternalId}, nil
 }
 

pkg/gateway/services/database.go

@@ -376,7 +376,7 @@ func (gws *GatewayService) recycleDependents(ctx context.Context, workspace *typ
 	return nil
 }
 
-// DeleteDatabaseService removes the deployment and its secrets; the disk is kept.
+// DeleteDatabaseService removes the deployments, secrets and app record; the disk is kept.
 func (gws *GatewayService) DeleteDatabaseService(ctx context.Context, authInfo *auth.AuthInfo, name string) error {
 	deployments, product, err := gws.databaseDeployments(ctx, authInfo.Workspace, name)
 	if err != nil {
@@ -396,7 +396,7 @@ func (gws *GatewayService) DeleteDatabaseService(ctx context.Context, authInfo *
 			return fmt.Errorf("delete secret %s: %w", secret, err)
 		}
 	}
-	return nil
+	return gws.backendRepo.DeleteApp(ctx, deployments[0].App.ExternalId)
 }
 
 // ListDatabaseServices returns the newest version of each database service.

pkg/runtime/runsc_test.go

@@ -409,7 +409,12 @@ case "$cmd" in
     cp "$RUNSC_FAKE_BUNDLE/config.json" "$RUNSC_FAKE_MOUNTS"
     ;;
   state)
-    printf '{"id":"container-1","pid":4321,"status":"running"}'
+    # No pid until restore has run: Restore returns on the first pid it sees.
+    if [ -f "$RUNSC_FAKE_MOUNTS" ]; then
+      printf '{"id":"container-1","pid":4321,"status":"running"}'
+    else
+      printf '{"id":"container-1","pid":0,"status":"created"}'
+    fi
     ;;
   wait|delete) ;;
   *)

sdk/src/beta9/cli/mcp.py

@@ -12,6 +12,7 @@
 import click
 
 from .. import terminal
+from ..channel import ServiceClient
 from ..config import get_config_context, get_settings
 from . import extraclick
 from .extraclick import ClickCommonGroup
@@ -34,13 +35,19 @@ def mcp():
 
 
 def _server(context: Optional[str]) -> Dict[str, str]:
+    """The MCP URL on the gateway's HTTP host, as the gateway reports it, plus the context token."""
     cfg = get_config_context(context or extraclick.selected_context())
     if not cfg.token:
         terminal.error(
             f"No token for this context; run `{terminal.cli_name()} configure` first.",
             code="NOT_AUTHENTICATED",
         )
-    return {"url": f"{cfg.http_url}/api/v1/mcp", "authorization": f"Bearer {cfg.token}"}
+    client = ServiceClient(cfg)
+    try:
+        base_url = client.http.base_url
+    finally:
+        client.close()
+    return {"url": f"{base_url}/api/v1/mcp", "authorization": f"Bearer {cfg.token}"}
 
 
 def _entry(client: str, server: Dict[str, str]) -> Dict[str, Any]: