fix: honor --discovery flag without --index

Add new branch to handle --discovery flag when --index is not provided.
Previously, the condition checked for both discoveryFlag AND indexSpecs,
causing the flag to be ignored when used alone. Now:

- discoveryFlag + indexSpecs: Discovery mode with remote + local indexes
- discoveryFlag alone: Discovery mode with local indexes only
- indexSpecs alone: Fixed mode with specified indexes
- No flags: Original behavior (fail fast if no indexes)

Applied fix to both stdioCommand and httpCommand handlers.

Agent-Id: agent-3635d277-f9a4-486b-81e0-cabd00c2a4b2

Author: richhankins

src/bin/cmd-mcp.ts

@@ -35,6 +35,11 @@ const stdioCommand = new Command("stdio")
         store = new ReadOnlyLayeredStore(localStore, remoteStore);
         indexNames = undefined; // Discovery mode: no fixed list
         discovery = true;
+      } else if (discoveryFlag) {
+        // Discovery mode with local indexes only
+        store = new FilesystemStore();
+        indexNames = undefined; // Discovery mode: no fixed list
+        discovery = true;
       } else if (indexSpecs && indexSpecs.length > 0) {
         // Fixed mode: use read-only CompositeStoreReader
         const specs = parseIndexSpecs(indexSpecs);
@@ -103,6 +108,11 @@ const httpCommand = new Command("http")
         store = new ReadOnlyLayeredStore(localStore, remoteStore);
         indexNames = undefined; // Discovery mode: no fixed list
         discovery = true;
+      } else if (discoveryFlag) {
+        // Discovery mode with local indexes only
+        store = new FilesystemStore();
+        indexNames = undefined; // Discovery mode: no fixed list
+        discovery = true;
       } else if (indexSpecs && indexSpecs.length > 0) {
         // Fixed mode: use read-only CompositeStoreReader
         const specs = parseIndexSpecs(indexSpecs);