fix: refresh shared indexer after knowledge base updates

src/index.ts

@@ -4,7 +4,6 @@ import { fileURLToPath } from "url";
 
 import { parseConfig } from "./config/schema.js";
 import { loadMergedConfig } from "./config/merger.js";
-import { Indexer } from "./indexer/index.js";
 import { createWatcherWithIndexer } from "./watcher/index.js";
 import {
   codebase_search,
@@ -20,10 +19,19 @@ import {
   add_knowledge_base,
   list_knowledge_bases,
   remove_knowledge_base,
+  getSharedIndexer,
   initializeTools,
 } from "./tools/index.js";
 import { loadCommandsFromDirectory } from "./commands/loader.js";
 import { hasProjectMarker } from "./utils/files.js";
+import type { CombinedWatcher } from "./watcher/index.js";
+
+let activeWatcher: CombinedWatcher | null = null;
+
+function replaceActiveWatcher(nextWatcher: CombinedWatcher | null): void {
+  activeWatcher?.stop();
+  activeWatcher = nextWatcher;
+}
 
 function getCommandsDir(): string {
   let currentDir = process.cwd();
@@ -43,7 +51,7 @@ const plugin: Plugin = async ({ directory }) => {
 
     initializeTools(projectRoot, config);
 
-    const indexer = new Indexer(projectRoot, config);
+    const indexer = getSharedIndexer();
 
     const isValidProject = !config.indexing.requireProjectMarker || hasProjectMarker(projectRoot);
 
@@ -61,7 +69,9 @@ const plugin: Plugin = async ({ directory }) => {
     }
 
     if (config.indexing.watchFiles && isValidProject) {
-      createWatcherWithIndexer(indexer, projectRoot, config);
+      replaceActiveWatcher(createWatcherWithIndexer(getSharedIndexer, projectRoot, config));
+    } else {
+      replaceActiveWatcher(null);
     }
 
     return {

src/tools/index.ts

@@ -1,7 +1,7 @@
 import { tool, type ToolDefinition } from "@opencode-ai/plugin";
 
+import { parseConfig, type ParsedCodebaseIndexConfig } from "../config/schema.js";
 import { Indexer } from "../indexer/index.js";
-import { ParsedCodebaseIndexConfig } from "../config/schema.js";
 import { formatCostEstimate } from "../utils/cost.js";
 import type { LogLevel } from "../config/schema.js";
 import type { LogEntry } from "../utils/logger.js";
@@ -30,6 +30,18 @@ export function initializeTools(projectRoot: string, config: ParsedCodebaseIndex
   sharedIndexer = new Indexer(projectRoot, config);
 }
 
+export function getSharedIndexer(): Indexer {
+  return getIndexer();
+}
+
+function refreshIndexerFromConfig(): void {
+  if (!sharedProjectRoot) {
+    throw new Error("Codebase index tools not initialized. Plugin may not be loaded correctly.");
+  }
+
+  sharedIndexer = new Indexer(sharedProjectRoot, parseConfig(loadConfig()));
+}
+
 function getIndexer(): Indexer {
   if (!sharedIndexer) {
     throw new Error("Codebase index tools not initialized. Plugin may not be loaded correctly.");
@@ -372,6 +384,7 @@ export const add_knowledge_base: ToolDefinition = tool({
     knowledgeBases.push(resolvedPath);
     config.knowledgeBases = knowledgeBases;
     saveConfig(config);
+    refreshIndexerFromConfig();
 
     let result = `${resolvedPath}\n`;
     result += `Total knowledge bases: ${knowledgeBases.length}\n`;
@@ -458,6 +471,7 @@ export const remove_knowledge_base: ToolDefinition = tool({
     const removed = knowledgeBases.splice(index, 1)[0];
     config.knowledgeBases = knowledgeBases;
     saveConfig(config);
+    refreshIndexerFromConfig();
 
     let result = `Removed: ${removed}\n\n`;
     result += `Remaining knowledge bases: ${knowledgeBases.length}\n`;

src/utils/files.ts

@@ -111,7 +111,16 @@ export function shouldIncludeFile(
 }
 
 function matchGlob(filePath: string, pattern: string): boolean {
-  let regexPattern = pattern
+  if (pattern.startsWith("**/")) {
+    const withoutPrefix = pattern.slice(3);
+    if (withoutPrefix && matchGlob(filePath, withoutPrefix)) {
+      return true;
+    }
+  }
+
+  const escapedPattern = pattern.replace(/[.+^$()|[\]\\]/g, "\\$&");
+
+  let regexPattern = escapedPattern
     .replace(/\*\*/g, "<<<DOUBLESTAR>>>")
     .replace(/\*/g, "[^/]*")
     .replace(/<<<DOUBLESTAR>>>/g, ".*")

src/watcher/index.ts

@@ -1,9 +1,9 @@
 import chokidar, { FSWatcher } from "chokidar";
 import * as path from "path";
 
-import { CodebaseIndexConfig } from "../config/schema.js";
+import type { CodebaseIndexConfig } from "../config/schema.js";
 import { createIgnoreFilter, shouldIncludeFile } from "../utils/files.js";
-import { Indexer } from "../indexer/index.js";
+import type { Indexer } from "../indexer/index.js";
 import { isGitRepo, getHeadPath, getCurrentBranch } from "../git/index.js";
 
 export type FileChangeType = "add" | "change" | "unlink";
@@ -243,7 +243,7 @@ export interface CombinedWatcher {
 }
 
 export function createWatcherWithIndexer(
-  indexer: Indexer,
+  getIndexer: () => Indexer,
   projectRoot: string,
   config: CodebaseIndexConfig
 ): CombinedWatcher {
@@ -256,7 +256,7 @@ export function createWatcherWithIndexer(
     const hasDelete = changes.some((c) => c.type === "unlink");
 
     if (hasAddOrChange || hasDelete) {
-      await indexer.index();
+      await getIndexer().index();
     }
   });
 
@@ -266,7 +266,7 @@ export function createWatcherWithIndexer(
     gitWatcher = new GitHeadWatcher(projectRoot);
     gitWatcher.start(async (oldBranch, newBranch) => {
       console.log(`Branch changed: ${oldBranch ?? "(none)"} -> ${newBranch}`);
-      await indexer.index();
+      await getIndexer().index();
     });
   }
 

tests/files.test.ts

@@ -82,6 +82,22 @@ describe("files utilities", () => {
         )
       ).toBe(false);
     });
+
+    it("should include root-level files with dots in their names", () => {
+      const filter = createIgnoreFilter(tempDir);
+      const includePatterns = ["**/*.{ts,tsx,js,jsx,mjs,cjs}"];
+      const excludePatterns = ["**/.*"];
+
+      expect(
+        shouldIncludeFile(
+          path.join(tempDir, "watcher.probe.ts"),
+          tempDir,
+          includePatterns,
+          excludePatterns,
+          filter
+        )
+      ).toBe(true);
+    });
   });
 
   describe("collectFiles", () => {

tests/tools-knowledge-bases.test.ts

@@ -0,0 +1,116 @@
+import * as fs from "fs";
+import * as os from "os";
+import * as path from "path";
+
+import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
+
+const { indexerInstances, MockIndexer } = vi.hoisted(() => {
+  const indexerInstances: Array<{ projectRoot: string; config: Record<string, unknown> }> = [];
+
+  class MockIndexer {
+    public readonly projectRoot: string;
+    public readonly config: Record<string, unknown>;
+
+    public constructor(projectRoot: string, config: Record<string, unknown>) {
+      this.projectRoot = projectRoot;
+      this.config = config;
+      indexerInstances.push({ projectRoot, config });
+    }
+
+    public estimateCost = vi.fn().mockResolvedValue({
+      filesCount: 0,
+      totalSizeBytes: 0,
+      estimatedChunks: 0,
+      estimatedTokens: 0,
+      estimatedCost: 0,
+      isFree: true,
+      provider: "ollama",
+      model: "nomic-embed-text",
+    });
+
+    public clearIndex = vi.fn().mockResolvedValue(undefined);
+    public index = vi.fn().mockResolvedValue({
+      totalFiles: 0,
+      totalChunks: 0,
+      indexedChunks: 0,
+      failedChunks: 0,
+      tokensUsed: 0,
+      durationMs: 0,
+      existingChunks: 0,
+      removedChunks: 0,
+      skippedFiles: [],
+      parseFailures: [],
+    });
+
+    public getStatus = vi.fn().mockResolvedValue({
+      indexed: true,
+      vectorCount: 0,
+      provider: "ollama",
+      model: "nomic-embed-text",
+      indexPath: "/tmp/index",
+      currentBranch: "main",
+      baseBranch: "main",
+    });
+
+    public healthCheck = vi.fn().mockResolvedValue({
+      removed: 0,
+      gcOrphanEmbeddings: 0,
+      gcOrphanChunks: 0,
+      gcOrphanSymbols: 0,
+      gcOrphanCallEdges: 0,
+      filePaths: [],
+    });
+
+    public getLogger = vi.fn().mockReturnValue({
+      isEnabled: vi.fn().mockReturnValue(false),
+      isMetricsEnabled: vi.fn().mockReturnValue(false),
+      getLogs: vi.fn().mockReturnValue([]),
+      getLogsByCategory: vi.fn().mockReturnValue([]),
+      getLogsByLevel: vi.fn().mockReturnValue([]),
+      formatMetrics: vi.fn().mockReturnValue(""),
+    });
+  }
+
+  return { indexerInstances, MockIndexer };
+});
+
+vi.mock("../src/indexer/index.js", () => ({
+  Indexer: MockIndexer,
+}));
+
+import { parseConfig } from "../src/config/schema.js";
+import { add_knowledge_base, initializeTools, remove_knowledge_base } from "../src/tools/index.js";
+
+describe("knowledge base tool config refresh", () => {
+  let tempDir: string;
+  let kbDir: string;
+
+  beforeEach(() => {
+    indexerInstances.length = 0;
+    tempDir = fs.mkdtempSync(path.join(os.tmpdir(), "kb-tools-test-"));
+    kbDir = fs.mkdtempSync(path.join(os.tmpdir(), "kb-source-"));
+    initializeTools(tempDir, parseConfig({ indexing: { watchFiles: false } }));
+  });
+
+  afterEach(() => {
+    fs.rmSync(tempDir, { recursive: true, force: true });
+    fs.rmSync(kbDir, { recursive: true, force: true });
+  });
+
+  it("rebuilds the shared indexer after adding a knowledge base", async () => {
+    await add_knowledge_base.execute({ path: kbDir });
+
+    expect(indexerInstances).toHaveLength(2);
+    expect(indexerInstances[1]?.projectRoot).toBe(tempDir);
+    expect(indexerInstances[1]?.config.knowledgeBases).toEqual([path.normalize(kbDir)]);
+  });
+
+  it("rebuilds the shared indexer after removing a knowledge base", async () => {
+    await add_knowledge_base.execute({ path: kbDir });
+    await remove_knowledge_base.execute({ path: kbDir });
+
+    expect(indexerInstances).toHaveLength(3);
+    expect(indexerInstances[2]?.projectRoot).toBe(tempDir);
+    expect(indexerInstances[2]?.config.knowledgeBases).toEqual([]);
+  });
+});

tests/watcher.test.ts

@@ -2,7 +2,7 @@ import { describe, it, expect, beforeEach, afterEach, vi } from "vitest";
 import * as fs from "fs";
 import * as path from "path";
 import * as os from "os";
-import { FileWatcher, GitHeadWatcher, FileChange } from "../src/watcher/index.js";
+import { FileWatcher, GitHeadWatcher, FileChange, createWatcherWithIndexer } from "../src/watcher/index.js";
 import { ParsedCodebaseIndexConfig } from "../src/config/schema.js";
 
 const createTestConfig = (overrides: Partial<ParsedCodebaseIndexConfig> = {}): ParsedCodebaseIndexConfig => ({
@@ -119,6 +119,73 @@ describe("FileWatcher", () => {
       expect(tsChanges.length).toBeGreaterThanOrEqual(0);
       expect(mdChanges.length).toBe(0);
     });
+
+    it("should include matching root-level files", async () => {
+      const changes: FileChange[] = [];
+      watcher = new FileWatcher(tempDir, createTestConfig({ include: ["**/*.ts"] }));
+
+      watcher.start(async (c) => {
+        changes.push(...c);
+      });
+
+      await new Promise((r) => setTimeout(r, 100));
+
+      fs.writeFileSync(path.join(tempDir, "root.ts"), "export const root = 1;");
+
+      await new Promise((r) => setTimeout(r, 1500));
+
+      expect(changes.some((c) => c.path.endsWith("root.ts"))).toBe(true);
+    });
+  });
+
+  describe("createWatcherWithIndexer", () => {
+    it("uses the latest indexer instance for file-triggered reindexing", async () => {
+      const staleIndexer = {
+        index: vi.fn().mockResolvedValue(undefined),
+      };
+      const refreshedIndexer = {
+        index: vi.fn().mockResolvedValue(undefined),
+      };
+
+      let currentIndexer = staleIndexer;
+      const combinedWatcher = createWatcherWithIndexer(
+        () => currentIndexer,
+        tempDir,
+        createTestConfig()
+      );
+
+      await new Promise((r) => setTimeout(r, 100));
+      currentIndexer = refreshedIndexer;
+
+      fs.writeFileSync(path.join(tempDir, "src", "reindex-me.ts"), "export const value = 1;");
+
+      await new Promise((r) => setTimeout(r, 1500));
+
+      expect(refreshedIndexer.index).toHaveBeenCalledTimes(1);
+      expect(staleIndexer.index).not.toHaveBeenCalled();
+
+      combinedWatcher.stop();
+    });
+
+    it("stops the watcher cleanly after start", () => {
+      const indexer = {
+        index: vi.fn().mockResolvedValue(undefined),
+      };
+
+      const combinedWatcher = createWatcherWithIndexer(
+        () => indexer,
+        tempDir,
+        createTestConfig()
+      );
+
+      expect(combinedWatcher.fileWatcher.isRunning()).toBe(true);
+      expect(combinedWatcher.gitWatcher?.isRunning() ?? false).toBe(false);
+
+      combinedWatcher.stop();
+
+      expect(combinedWatcher.fileWatcher.isRunning()).toBe(false);
+      expect(combinedWatcher.gitWatcher?.isRunning() ?? false).toBe(false);
+    });
   });
 });