Publisher-managed "deleted" support (#893)

(Updated auto-generated PR description from @tadasant / Claude on Feb
22, 2026)

## Motivation and Context

Fixes #637

Server lifecycle management (deprecation and yanking) is a standard
requirement for package registries. Use cases like rebranding, security
vulnerabilities, and end-of-life servers demand the ability to mark
servers as deprecated or deleted, with optional messaging to guide
consumers toward alternatives.

## Changes

### New API endpoints

- **`PATCH /v0/servers/{serverName}/versions/{version}/status`** —
Update the lifecycle status of a single server version
- **`PATCH /v0/servers/{serverName}/status`** — Update the lifecycle
status of all versions of a server in a single transaction

Both endpoints accept:
```json
{
  "status": "active|deprecated|deleted",
  "statusMessage": "Optional message (max 500 chars) explaining the change"
}
```

### New CLI command

- **`mcp-publisher status <serverName> [version]`** — Update server
lifecycle status from the command line
  - `--status` (required): `active`, `deprecated`, or `deleted`
  - `--message`: Optional status message
- `--all-versions`: Apply to all versions of the server (replaces the
`<version>` argument)

### API response changes

`RegistryExtensions` now includes two new fields:
- `statusChangedAt` — Timestamp of the last status change
- `statusMessage` — Optional free-form message (e.g., deprecation
reason, migration guidance)

### List endpoint changes

- New `include_deleted` query parameter on `GET /v0/servers` — defaults
to `false`, hiding deleted servers from listings
- When `updated_since` is provided, `include_deleted` is automatically
set to `true` for incremental sync

### Database

- Migration `013_add_status_fields.sql`: Adds `status_changed_at` (NOT
NULL, initialized from `published_at`) and `status_message` columns to
the `servers` table

### Design decisions (from review discussion)

- **Dedicated status endpoints** rather than overloading the existing
edit endpoint
- **Bidirectional status transitions** — all transitions between
`active`, `deprecated`, and `deleted` are allowed
- **`statusMessage` as free-form text** — no structured `nextName` or
`alternativeUrl` fields (per maintainer feedback, to avoid complexity
around chaining, trust transfer, etc.)
- **Publish permission** grants status change access (not limited to
admin/edit)
- **Status message auto-cleared** when transitioning back to `active`
Good, now I have the full picture. Here's the addendum:

### Consumer-facing API changes

The new status fields live inside
`_meta["io.modelcontextprotocol.registry/official"]` on every
`ServerResponse`. This is the existing `RegistryExtensions` object — two
new fields are added alongside the existing ones:

**Before:**
```json
{
  "server": { "name": "com.example/my-server", "...": "..." },
  "_meta": {
    "io.modelcontextprotocol.registry/official": {
      "status": "active",
      "publishedAt": "2025-06-01T00:00:00Z",
      "updatedAt": "2025-06-15T00:00:00Z",
      "isLatest": true
    }
  }
}
```

**After:**
```json
{
  "server": { "name": "com.example/my-server", "...": "..." },
  "_meta": {
    "io.modelcontextprotocol.registry/official": {
      "status": "deprecated",
      "statusChangedAt": "2026-02-01T12:00:00Z",
      "statusMessage": "Deprecated in favor of com.example/my-server-v2",
      "publishedAt": "2025-06-01T00:00:00Z",
      "updatedAt": "2026-02-01T12:00:00Z",
      "isLatest": true
    }
  }
}
```

| New field | Type | Present when |
|-----------|------|-------------|
| `statusChangedAt` | `string` (RFC3339) | Always — initialized to
`publishedAt` for existing records |
| `statusMessage` | `string` (max 500 chars) | Only when set —
`null`/omitted for active servers (auto-cleared on transition to active)
|

These fields appear on **every endpoint that returns a
`ServerResponse`**: `GET /v0/servers`, `GET /v0/servers/{name}`, `GET
/v0/servers/{name}/versions/{version}`, and the new PATCH status
endpoints.

### List endpoint filtering

`GET /v0/servers` gains an `include_deleted` query parameter:

| Scenario | Behavior |
|----------|----------|
| No `include_deleted` param | Deleted servers hidden (default `false`)
|
| `include_deleted=true` | Deleted servers included in results |
| `updated_since` provided | `include_deleted` forced to `true` for
incremental sync |

## How Has This Been Tested?

- Unit tests for status handler (`status_test.go`) covering status
transitions, permission checks, validation errors, and the all-versions
endpoint
- Unit tests for the CLI command (`status_test.go`)
- Integration with existing server/edit handler tests
- Database layer tests for the new status update and query methods
- Tested locally with `make dev-compose`

## Types of changes

- [x] New feature (non-breaking change which adds functionality)

## Checklist

- [x] I have read the [MCP
Documentation](https://modelcontextprotocol.io)
- [x] My code follows the repository's style guidelines
- [x] New and existing tests pass locally
- [x] I have added appropriate error handling
- [x] I have added or updated documentation as needed

## Open items from review

- [ ] `include_deleted` silent override: When `updated_since` is
provided and `include_deleted=false` is explicitly passed, should return
a 400 error rather than silently overriding
([thread](https://github.com/modelcontextprotocol/registry/pull/893#discussion_r2100879360))
— agreed upon but may not yet be implemented

internal/database/database.go

@@ -7,6 +7,7 @@ import (
 
 	"github.com/jackc/pgx/v5"
 	apiv0 "github.com/modelcontextprotocol/registry/pkg/api/v0"
+	"github.com/modelcontextprotocol/registry/pkg/model"
 )
 
 // Common database errors
@@ -21,12 +22,13 @@ var (
 
 // ServerFilter defines filtering options for server queries
 type ServerFilter struct {
-	Name          *string    // for finding versions of same server
-	RemoteURL     *string    // for duplicate URL detection
-	UpdatedSince  *time.Time // for incremental sync filtering
-	SubstringName *string    // for substring search on name
-	Version       *string    // for exact version matching
-	IsLatest      *bool      // for filtering latest versions only
+	Name           *string    // for finding versions of same server
+	RemoteURL      *string    // for duplicate URL detection
+	UpdatedSince   *time.Time // for incremental sync filtering
+	SubstringName  *string    // for substring search on name
+	Version        *string    // for exact version matching
+	IsLatest       *bool      // for filtering latest versions only
+	IncludeDeleted *bool      // for including deleted packages in results (default: exclude)
 }
 
 // Database defines the interface for database operations
@@ -36,15 +38,17 @@ type Database interface {
 	// UpdateServer updates an existing server record
 	UpdateServer(ctx context.Context, tx pgx.Tx, serverName, version string, serverJSON *apiv0.ServerJSON) (*apiv0.ServerResponse, error)
 	// SetServerStatus updates the status of a specific server version
-	SetServerStatus(ctx context.Context, tx pgx.Tx, serverName, version string, status string) (*apiv0.ServerResponse, error)
+	SetServerStatus(ctx context.Context, tx pgx.Tx, serverName, version string, status model.Status, statusMessage *string) (*apiv0.ServerResponse, error)
+	// SetAllVersionsStatus updates the status of all versions of a server in a single query
+	SetAllVersionsStatus(ctx context.Context, tx pgx.Tx, serverName string, status model.Status, statusMessage *string) ([]*apiv0.ServerResponse, error)
 	// ListServers retrieve server entries with optional filtering
 	ListServers(ctx context.Context, tx pgx.Tx, filter *ServerFilter, cursor string, limit int) ([]*apiv0.ServerResponse, string, error)
 	// GetServerByName retrieve a single server by its name
-	GetServerByName(ctx context.Context, tx pgx.Tx, serverName string) (*apiv0.ServerResponse, error)
+	GetServerByName(ctx context.Context, tx pgx.Tx, serverName string, includeDeleted bool) (*apiv0.ServerResponse, error)
 	// GetServerByNameAndVersion retrieve specific version of a server by server name and version
-	GetServerByNameAndVersion(ctx context.Context, tx pgx.Tx, serverName string, version string) (*apiv0.ServerResponse, error)
+	GetServerByNameAndVersion(ctx context.Context, tx pgx.Tx, serverName string, version string, includeDeleted bool) (*apiv0.ServerResponse, error)
 	// GetAllVersionsByServerName retrieve all versions of a server by server name
-	GetAllVersionsByServerName(ctx context.Context, tx pgx.Tx, serverName string) ([]*apiv0.ServerResponse, error)
+	GetAllVersionsByServerName(ctx context.Context, tx pgx.Tx, serverName string, includeDeleted bool) ([]*apiv0.ServerResponse, error)
 	// GetCurrentLatestVersion retrieve the current latest version of a server by server name
 	GetCurrentLatestVersion(ctx context.Context, tx pgx.Tx, serverName string) (*apiv0.ServerResponse, error)
 	// CountServerVersions count the number of versions for a server