Replace agent-managed with discovery mode

- Replace --agent-managed flag with --discovery in cmd-mcp.ts
- Remove index_repo and delete_index tool handlers from mcp-server.ts
- Delete layered-store.ts and layered-store.test.ts files
- Keep list_indexes in both modes
- Use withListIndexesReference() in discovery mode, withIndexList() in fixed mode
- Update MCPServerConfig to use discovery flag instead of agentManaged
- All tests pass, build succeeds

Agent-Id: agent-84f44748-891f-477f-b3f3-c078cb5bd2c5

Author: richhankins

src/bin/cmd-mcp.ts

@@ -7,7 +7,6 @@ import { FilesystemStore } from "../stores/filesystem.js";
 import { runMCPServer } from "../clients/mcp-server.js";
 import { parseIndexSpecs } from "../stores/index-spec.js";
 import { CompositeStoreReader } from "../stores/composite.js";
-import { LayeredStore } from "../stores/index.js";
 
 // stdio subcommand (stdio-based MCP server for local clients like Claude Desktop)
 const stdioCommand = new Command("stdio")
@@ -16,12 +15,12 @@ const stdioCommand = new Command("stdio")
     "-i, --index <specs...>",
     "Index spec(s): name, path:/path, or s3://bucket/key"
   )
-  .option("--agent-managed", "Enable dynamic index management (index_repo, delete_index)")
+  .option("--discovery", "Enable discovery mode (read-only, manage indexes via CLI)")
   .option("--search-only", "Disable list_files/read_file tools (search only)")
   .action(async (options) => {
     try {
       const indexSpecs: string[] | undefined = options.index;
-      const agentManaged = options.agentManaged || !indexSpecs || indexSpecs.length === 0;
+      const discovery = options.discovery || !indexSpecs || indexSpecs.length === 0;
 
       let store;
       let indexNames: string[] | undefined;
@@ -31,29 +30,23 @@ const stdioCommand = new Command("stdio")
         const specs = parseIndexSpecs(indexSpecs);
         indexNames = specs.map((s) => s.displayName);
 
-        if (agentManaged) {
-          // Agent-managed + remote indexes: use LayeredStore
-          const remoteStore = await CompositeStoreReader.fromSpecs(specs);
-          store = new LayeredStore(new FilesystemStore(), remoteStore);
-        } else {
-          // Fixed mode: use read-only CompositeStoreReader
-          store = await CompositeStoreReader.fromSpecs(specs);
-        }
+        // Fixed mode: use read-only CompositeStoreReader
+        store = await CompositeStoreReader.fromSpecs(specs);
       } else {
-        // No --index: use FilesystemStore (agent-managed mode)
+        // No --index: use FilesystemStore (discovery mode)
         store = new FilesystemStore();
-        // Dynamic indexing: server can start with zero indexes
-        // Use list_indexes to see available indexes, index_repo to create new ones
+        // Discovery mode: server can start with zero indexes
+        // Use list_indexes to see available indexes, manage via CLI
         indexNames = undefined;
       }
 
       // Start MCP server (writes to stdout, reads from stdin)
-      // agentManaged: true when no -i flags (dynamic mode), false when -i flags provided (fixed mode)
+      // discovery: true when no -i flags (discovery mode), false when -i flags provided (fixed mode)
       await runMCPServer({
         store,
         indexNames,
         searchOnly: options.searchOnly,
-        agentManaged,
+        discovery,
       });
     } catch (error) {
       // Write errors to stderr (stdout is for MCP protocol)
@@ -69,7 +62,7 @@ const httpCommand = new Command("http")
     "-i, --index <specs...>",
     "Index spec(s): name, path:/path, or s3://bucket/key"
   )
-  .option("--agent-managed", "Enable dynamic index management (index_repo, delete_index)")
+  .option("--discovery", "Enable discovery mode (read-only, manage indexes via CLI)")
   .option("--port <number>", "Port to listen on", "3000")
   .option("--host <host>", "Host to bind to", "localhost")
   .option("--cors <origins>", "CORS origins (comma-separated, or '*' for any)")
@@ -82,7 +75,7 @@ const httpCommand = new Command("http")
   .action(async (options) => {
     try {
       const indexSpecs: string[] | undefined = options.index;
-      const agentManaged = options.agentManaged || !indexSpecs || indexSpecs.length === 0;
+      const discovery = options.discovery || !indexSpecs || indexSpecs.length === 0;
 
       let store;
       let indexNames: string[] | undefined;
@@ -92,19 +85,13 @@ const httpCommand = new Command("http")
         const specs = parseIndexSpecs(indexSpecs);
         indexNames = specs.map((s) => s.displayName);
 
-        if (agentManaged) {
-          // Agent-managed + remote indexes: use LayeredStore
-          const remoteStore = await CompositeStoreReader.fromSpecs(specs);
-          store = new LayeredStore(new FilesystemStore(), remoteStore);
-        } else {
-          // Fixed mode: use read-only CompositeStoreReader
-          store = await CompositeStoreReader.fromSpecs(specs);
-        }
+        // Fixed mode: use read-only CompositeStoreReader
+        store = await CompositeStoreReader.fromSpecs(specs);
       } else {
-        // No --index: use FilesystemStore (agent-managed mode)
+        // No --index: use FilesystemStore (discovery mode)
         store = new FilesystemStore();
-        // Dynamic indexing: server can start with zero indexes
-        // Use list_indexes to see available indexes, index_repo to create new ones
+        // Discovery mode: server can start with zero indexes
+        // Use list_indexes to see available indexes, manage via CLI
         indexNames = undefined;
       }
 
@@ -121,13 +108,13 @@ const httpCommand = new Command("http")
       const apiKey = options.apiKey ?? process.env.MCP_API_KEY;
 
       // Start HTTP server
-      // agentManaged: true when no -i flags (dynamic mode), false when -i flags provided (fixed mode)
+      // discovery: true when no -i flags (discovery mode), false when -i flags provided (fixed mode)
       const { runMCPHttpServer } = await import("../clients/mcp-http-server.js");
       const server = await runMCPHttpServer({
         store,
         indexNames,
         searchOnly: options.searchOnly,
-        agentManaged,
+        discovery,
         port: parseInt(options.port, 10),
         host: options.host,
         cors,

src/clients/mcp-server.ts

@@ -74,12 +74,12 @@ export interface MCPServerConfig {
    */
   version?: string;
   /**
-   * Agent-managed mode flag.
-   * When true: use withListIndexesReference (no enum in schemas)
-   * When false/undefined: use withIndexList (include enum in schemas)
+   * Discovery mode flag.
+   * When true: use withListIndexesReference (no enum in schemas), no write tools
+   * When false/undefined: use withIndexList (include enum in schemas), write tools available
    * @default false
    */
-  agentManaged?: boolean;
+  discovery?: boolean;
 }
 
 /**
@@ -140,13 +140,13 @@ export async function createMCPServer(
     };
   };
 
-  // Tool descriptions: use enum in fixed mode, reference in agent-managed mode
+  // Tool descriptions: use enum in fixed mode, reference in discovery mode
   let searchDescription: string;
   let listFilesDescription: string;
   let readFileDescription: string;
 
-  if (config.agentManaged) {
-    // Agent-managed mode: use reference to list_indexes (no enum)
+  if (config.discovery) {
+    // Discovery mode: use reference to list_indexes (no enum)
     searchDescription = withListIndexesReference(SEARCH_DESCRIPTION);
     listFilesDescription = withListIndexesReference(LIST_FILES_DESCRIPTION);
     readFileDescription = withListIndexesReference(READ_FILE_DESCRIPTION);
@@ -179,7 +179,7 @@ export async function createMCPServer(
             index_name: {
               type: "string",
               description: "Name of the index to search.",
-              ...(config.agentManaged ? {} : { enum: runner.indexes.map(i => i.name) }),
+              ...(config.discovery ? {} : { enum: runner.indexes.map(i => i.name) }),
             },
             query: {
               type: "string",
@@ -195,71 +195,6 @@ export async function createMCPServer(
       },
     ];
 
-    // Add index_repo if store supports write operations
-    if ('save' in config.store) {
-      tools.push({
-        name: "index_repo",
-        description: "Create or update an index from a repository. This may take 30+ seconds for large repos. The index will be available for search, list_files, and read_file after creation.",
-        inputSchema: {
-          type: "object",
-          properties: {
-            name: {
-              type: "string",
-              description: "Unique name for this index (e.g., 'pytorch', 'my-lib')"
-            },
-            source_type: {
-              type: "string",
-              enum: ["github", "gitlab", "bitbucket", "website"],
-              description: "Type of source to index"
-            },
-            owner: {
-              type: "string",
-              description: "GitHub repository owner (required for github)"
-            },
-            repo: {
-              type: "string",
-              description: "Repository name (required for github, bitbucket)"
-            },
-            project_id: {
-              type: "string",
-              description: "GitLab project ID or path (required for gitlab)"
-            },
-            workspace: {
-              type: "string",
-              description: "BitBucket workspace slug (required for bitbucket)"
-            },
-            url: {
-              type: "string",
-              description: "URL to crawl (required for website)"
-            },
-            ref: {
-              type: "string",
-              description: "Branch, tag, or commit (default: HEAD)"
-            },
-          },
-          required: ["name", "source_type"],
-        },
-      });
-    }
-
-    // Add delete_index if store supports it
-    if ('delete' in config.store) {
-      tools.push({
-        name: "delete_index",
-        description: "Delete an index by name. This removes the index from storage and it will no longer be available for search.",
-        inputSchema: {
-          type: "object",
-          properties: {
-            name: {
-              type: "string",
-              description: "Name of the index to delete",
-            },
-          },
-          required: ["name"],
-        },
-      });
-    }
-
     // Only advertise file tools if not in search-only mode
     if (!searchOnly) {
       tools.push(
@@ -272,7 +207,7 @@ export async function createMCPServer(
               index_name: {
                 type: "string",
                 description: "Name of the index.",
-                ...(config.agentManaged ? {} : { enum: runner.indexes.map(i => i.name) }),
+                ...(config.discovery ? {} : { enum: runner.indexes.map(i => i.name) }),
               },
               directory: {
                 type: "string",
@@ -303,7 +238,7 @@ export async function createMCPServer(
               index_name: {
                 type: "string",
                 description: "Name of the index.",
-                ...(config.agentManaged ? {} : { enum: runner.indexes.map(i => i.name) }),
+                ...(config.discovery ? {} : { enum: runner.indexes.map(i => i.name) }),
               },
               path: {
                 type: "string",
@@ -364,123 +299,6 @@ export async function createMCPServer(
       };
     }
 
-    // Handle delete_index separately (uses 'name' not 'index_name')
-    if (name === "delete_index") {
-      const indexName = args?.name as string;
-
-      if (!indexName) {
-        return { content: [{ type: "text", text: "Error: name is required" }], isError: true };
-      }
-
-      // Check if index exists
-      if (!runner.indexNames.includes(indexName)) {
-        return {
-          content: [{ type: "text", text: `Error: Index "${indexName}" not found` }],
-          isError: true,
-        };
-      }
-
-      // Check if store supports delete operations
-      if (!('delete' in config.store)) {
-        return { content: [{ type: "text", text: "Error: Store does not support delete operations" }], isError: true };
-      }
-
-      try {
-        // Delete from store
-        await (config.store as IndexStore).delete(indexName);
-
-        // Refresh runner state
-        await runner.refreshIndexList();
-        runner.invalidateClient(indexName);
-
-        return {
-          content: [{ type: "text", text: `Deleted index "${indexName}"` }],
-        };
-      } catch (error) {
-        return { content: [{ type: "text", text: `Error deleting index: ${error}` }], isError: true };
-      }
-    }
-
-    // Handle index_repo separately (uses 'name' not 'index_name')
-    if (name === "index_repo") {
-      const indexName = args?.name as string;
-      const sourceType = args?.source_type as string;
-
-      if (!indexName) {
-        return { content: [{ type: "text", text: "Error: name is required" }], isError: true };
-      }
-      if (!sourceType) {
-        return { content: [{ type: "text", text: "Error: source_type is required" }], isError: true };
-      }
-
-      try {
-        let source: Source;
-        let sourceDesc: string;
-
-        if (sourceType === "github") {
-          const owner = args?.owner as string;
-          const repo = args?.repo as string;
-          if (!owner || !repo) {
-            return { content: [{ type: "text", text: "Error: github requires owner and repo" }], isError: true };
-          }
-          const { GitHubSource } = await import("../sources/github.js");
-          source = new GitHubSource({ owner, repo, ref: (args?.ref as string) || "HEAD" });
-          sourceDesc = `github://${owner}/${repo}`;
-        } else if (sourceType === "gitlab") {
-          const projectId = args?.project_id as string;
-          if (!projectId) {
-            return { content: [{ type: "text", text: "Error: gitlab requires project_id" }], isError: true };
-          }
-          const { GitLabSource } = await import("../sources/gitlab.js");
-          source = new GitLabSource({ projectId, ref: (args?.ref as string) || "HEAD" });
-          sourceDesc = `gitlab://${projectId}`;
-        } else if (sourceType === "bitbucket") {
-          const workspace = args?.workspace as string;
-          const repo = args?.repo as string;
-          if (!workspace || !repo) {
-            return { content: [{ type: "text", text: "Error: bitbucket requires workspace and repo" }], isError: true };
-          }
-          const { BitBucketSource } = await import("../sources/bitbucket.js");
-          source = new BitBucketSource({ workspace, repo, ref: (args?.ref as string) || "HEAD" });
-          sourceDesc = `bitbucket://${workspace}/${repo}`;
-        } else if (sourceType === "website") {
-          const url = args?.url as string;
-          if (!url) {
-            return { content: [{ type: "text", text: "Error: website requires url" }], isError: true };
-          }
-          const { WebsiteSource } = await import("../sources/website.js");
-          source = new WebsiteSource({ url });
-          sourceDesc = `website://${url}`;
-        } else {
-          return { content: [{ type: "text", text: `Error: Unknown source_type: ${sourceType}` }], isError: true };
-        }
-
-        // Run indexer - need IndexStore for this
-        const { Indexer } = await import("../core/indexer.js");
-        const indexer = new Indexer();
-
-        // Check if store supports write operations
-        if (!('save' in config.store)) {
-          return { content: [{ type: "text", text: "Error: Store does not support write operations (index_repo requires IndexStore)" }], isError: true };
-        }
-
-        const result = await indexer.index(source, config.store as IndexStore, indexName);
-
-        // Refresh runner state
-        await runner.refreshIndexList();
-        runner.invalidateClient(indexName);
-
-        return {
-          content: [{
-            type: "text",
-            text: `Created index "${indexName}" from ${sourceDesc}\n- Type: ${result.type}\n- Files indexed: ${result.filesIndexed}\n- Duration: ${result.duration}ms`
-          }],
-        };
-      } catch (error) {
-        return { content: [{ type: "text", text: `Error indexing: ${error}` }], isError: true };
-      }
-    }
-
     try {
       const indexName = args?.index_name as string;
       const client = await runner.getClient(indexName);

src/stores/index.ts

@@ -10,7 +10,6 @@ export type { MemoryStoreConfig } from "./memory.js";
 export { S3Store } from "./s3.js";
 export type { S3StoreConfig } from "./s3.js";
 export { CompositeStoreReader } from "./composite.js";
-export { LayeredStore } from "./layered-store.js";
 export { parseIndexSpec, parseIndexSpecs } from "./index-spec.js";
 export type { IndexSpec } from "./index-spec.js";