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

docs/reference/cli/commands.md

@@ -276,6 +276,51 @@ mcp-publisher publish
 mcp-publisher publish ./config/server.json
 ```
 
+### `mcp-publisher status`
+
+Update the lifecycle status of a published server.
+
+**Usage:**
+```bash
+mcp-publisher status --status <active|deprecated|deleted> [flags] <server-name> [version]
+```
+
+**Flags:**
+- `--status` (required) - New status: `active`, `deprecated`, or `deleted`
+- `--message` - Optional message explaining the status change (not allowed when status is `active`)
+- `--all-versions` - Apply status change to all versions of the server
+- `--yes`, `-y` - Skip confirmation prompt (only applies when using `--all-versions`)
+
+**Arguments:**
+- `server-name` - Full server name (e.g., `io.github.user/my-server`)
+- `version` - Server version to update (required unless `--all-versions` is set)
+
+**Status Values:**
+- `active` - Server is active and visible in default listings
+- `deprecated` - Server is deprecated but still visible with a warning message
+- `deleted` - Server is hidden from default listings
+
+**Examples:**
+```bash
+# Deprecate a specific version
+mcp-publisher status --status deprecated --message "Please upgrade to 2.0.0" \
+  io.github.user/my-server 1.0.0
+
+# Delete a version with security issues
+mcp-publisher status --status deleted --message "Critical security vulnerability" \
+  io.github.user/my-server 1.0.0
+
+# Restore a version to active
+mcp-publisher status --status active io.github.user/my-server 1.0.0
+
+# Deprecate all versions at once
+mcp-publisher status --status deprecated --all-versions --message "Project archived" \
+  io.github.user/my-server
+```
+
+**Requirements:**
+- Must be logged in with `publish` or `edit` permission for the server namespace
+
 ### `mcp-publisher logout`
 
 Clear stored authentication credentials.