feat: Update Claude instructions to discourage direct codegraph tool usage in main session

Changes guidance to recommend spawning Explore agents for exploration questions instead of using codegraph_explore/codegraph_context directly in main session to avoid filling up context with large amounts of source code. Adds completeness signal to codegraph_explore output so agents know not to re-read files that already have source code included.

src/mcp/tools.ts

@@ -849,6 +849,11 @@ export class ToolHandler {
       }
     }
 
+    // Add completeness signal so agents know they don't need to re-read these files
+    lines.push('');
+    lines.push('---');
+    lines.push(`> **Complete source code is included above for ${filesIncluded} files.** You do NOT need to re-read these files — the relevant sections are already shown in full. Only use Read/Grep for files listed under "Additional relevant files" if you need more detail.`);
+
     return this.textResult(lines.join('\n'));
   }