Fix agentManaged config calculation in cmd-mcp.ts

The agentManaged flag was correctly calculated at the top of both stdio and http handlers, but then recalculated incorrectly when passing to the MCP server config. This caused the --agent-managed flag to be ignored when combined with -i specs.

Changes:
- Line 56 (stdio): Use calculated agentManaged variable instead of recalculating
- Line 130 (http): Use calculated agentManaged variable instead of recalculating

This ensures --agent-managed -i s3://... correctly sets agentManaged: true in the server config.

Agent-Id: agent-1fdc5885-eb2c-4a33-9451-323cf14bb29a

Author: richhankins

src/bin/cmd-mcp.ts

@@ -53,7 +53,7 @@ const stdioCommand = new Command("stdio")
         store,
         indexNames,
         searchOnly: options.searchOnly,
-        agentManaged: !indexSpecs || indexSpecs.length === 0,
+        agentManaged,
       });
     } catch (error) {
       // Write errors to stderr (stdout is for MCP protocol)
@@ -127,7 +127,7 @@ const httpCommand = new Command("http")
         store,
         indexNames,
         searchOnly: options.searchOnly,
-        agentManaged: !indexSpecs || indexSpecs.length === 0,
+        agentManaged,
         port: parseInt(options.port, 10),
         host: options.host,
         cors,