perf(db): use pk id for lookups and ordering (#390)

summary
- use the indexed primary key (`id`) for `getbyid`, `updateserver`, and
list ordering/cursor, instead of extracting `_meta...id` from jsonb
- in `updateserver`, error if the body tries to change the id; set
`meta.official.id` when missing

changes
- database: `getbyid` → `where id = $1`
- database: `updateserver` → `where id = $2`; fail on id mismatch; set
id if missing
- database: `list` orders by `id` and paginates via `id > $cursor`
- no schema or api changes

<details>
<summary>performance</summary>

- env: repo docker compose postgres, 5k–10k rows, warm cache
- getbyid: `id` ≈ 0.02 ms vs jsonb path ≈ 0.80 ms
- update: `id` ≈ 0.15 ms vs jsonb path ≈ 0.78 ms
- list (limit 100): order by `id` ≈ 0.13 ms vs jsonb path id ≈ 2.24 ms
(~17x slower)

</details>

<details>
<summary>explain analyze snippets</summary>

getbyid by `id`
```
Index Scan using idx_benchmark_servers_id on benchmark_servers (actual time≈0.01–0.02 ms)
Buffers: shared hit≈3
```

getbyid by jsonb path
```
Seq Scan on benchmark_servers (actual time≈0.43–0.83 ms)
Filter: ((value->'_meta'->'io.modelcontextprotocol.registry/official'->>'id') = $1)
Rows Removed by Filter: ≈4999
Buffers: shared hit≈455
```

update by `id`
```
Update on benchmark_servers …
-> Index Scan using idx_benchmark_servers_id … (actual time≈0.007 ms)
Execution Time: ≈0.15 ms
```

update by jsonb path
```
Update on benchmark_servers …
-> Seq Scan on benchmark_servers … Rows Removed by Filter: ≈4999
Execution Time: ≈0.78 ms
```
</details>

<details>
<summary>reproduce quickly</summary>

- start postgres: `docker compose up -d postgres`
- create a simple table (id varchar pk, value jsonb) with several
thousand rows
- compare plans: `explain (analyze, buffers) select value from … where
id = $1` vs the jsonb path predicate
</details>

---------

Co-authored-by: Adam Jones <[email protected]>

Author: zzstoatzz

internal/database/postgres.go

@@ -94,12 +94,12 @@ func (db *PostgreSQL) List(
 		}
 	}
 
-	// Add cursor pagination using registry metadata ID
+	// Add cursor pagination using primary key ID
 	if cursor != "" {
 		if _, err := uuid.Parse(cursor); err != nil {
 			return nil, "", fmt.Errorf("invalid cursor format: %w", err)
 		}
-		whereConditions = append(whereConditions, fmt.Sprintf("(value->'_meta'->'io.modelcontextprotocol.registry/official'->>'id') > $%d", argIndex))
+		whereConditions = append(whereConditions, fmt.Sprintf("id > $%d", argIndex))
 		args = append(args, cursor)
 		argIndex++
 	}
@@ -112,12 +112,12 @@ func (db *PostgreSQL) List(
 
 	// Simple query on servers table
 	query := fmt.Sprintf(`
-		SELECT value
-		FROM servers
-		%s
-		ORDER BY (value->'_meta'->'io.modelcontextprotocol.registry/official'->>'id')
-		LIMIT $%d
-	`, whereClause, argIndex)
+        SELECT value
+        FROM servers
+        %s
+        ORDER BY id
+        LIMIT $%d
+    `, whereClause, argIndex)
 	args = append(args, limit)
 
 	rows, err := db.conn.Query(ctx, query, args...)
@@ -168,7 +168,7 @@ func (db *PostgreSQL) GetByID(ctx context.Context, id string) (*apiv0.ServerJSON
 	query := `
 		SELECT value
 		FROM servers
-		WHERE (value->'_meta'->'io.modelcontextprotocol.registry/official'->>'id') = $1
+		WHERE id = $1
 	`
 
 	var valueJSON []byte
@@ -230,6 +230,11 @@ func (db *PostgreSQL) UpdateServer(ctx context.Context, id string, server *apiv0
 		return nil, ctx.Err()
 	}
 
+	// Validate that meta structure exists and ID matches path
+	if server.Meta == nil || server.Meta.Official == nil || server.Meta.Official.ID != id {
+		return nil, fmt.Errorf("%w: io.modelcontextprotocol.registry/official.id must match path id (%s)", ErrInvalidInput, id)
+	}
+
 	// Marshal updated server
 	valueJSON, err := json.Marshal(server)
 	if err != nil {
@@ -240,7 +245,7 @@ func (db *PostgreSQL) UpdateServer(ctx context.Context, id string, server *apiv0
 	query := `
 		UPDATE servers 
 		SET value = $1
-		WHERE (value->'_meta'->'io.modelcontextprotocol.registry/official'->>'id') = $2
+		WHERE id = $2
 	`
 
 	result, err := db.conn.Exec(ctx, query, valueJSON, id)