@zilliz/claude-context-mcp 0.1.11 → 0.1.13

package/README.md

@@ -100,7 +100,7 @@ Google's Gemini provides competitive embeddings with good multilingual support.
 # Required: Your Gemini API key
 GEMINI_API_KEY=your-gemini-api-key
 
-# Optional: Specify embedding model (default: gemini-embedding-001)
+# Optional: Specify embedding model (default: gemini-embedding-001; supports gemini-embedding-2)
 EMBEDDING_MODEL=gemini-embedding-001
 
 # Optional: Custom API base URL (for custom endpoints)
@@ -130,6 +130,9 @@ EMBEDDING_MODEL=nomic-embed-text
 
 # Optional: Specify Ollama host (default: http://127.0.0.1:11434)
 OLLAMA_HOST=http://127.0.0.1:11434
+
+# Optional: Override embedding dimension to skip runtime dimension detection
+EMBEDDING_DIMENSION=768
 ```
 
 **Setup Instructions:**
@@ -197,6 +200,49 @@ CODE_CHUNKS_COLLECTION_NAME_OVERRIDE=my_project
 
 The per-codebase `<pathHash>` suffix is preserved even when the override is set, so the same MCP server can still index multiple repos without collapsing them onto one collection. The override value is sanitized to letters, numbers, and underscores, and truncated to keep the full name within Milvus's 255-char limit. If you unset the variable later, Claude Context switches back to the plain `code_chunks_<pathHash>` naming.
 
+#### Trigger File Watcher (Optional)
+
+In addition to the periodic background sync, the MCP server watches a sentinel file at `~/.context/.sync-trigger` and starts an immediate re-index whenever the file is modified. This lets external tools (Claude Code `PostToolUse` hooks, editor save hooks, CI scripts, etc.) request a sync on demand instead of waiting for the next polling tick.
+
+```bash
+# Default: watcher enabled. Set to false to disable filesystem watching entirely
+# (useful on read-only filesystems or sandboxed environments).
+CLAUDE_CONTEXT_TRIGGER_WATCHER=true
+```
+
+Example — Claude Code hook that re-indexes after every Edit/Write:
+
+```json
+"hooks": {
+  "PostToolUse": [
+    { "matcher": "Edit|Write", "hooks": [
+      { "type": "command", "command": "touch ~/.context/.sync-trigger" }
+    ]}
+  ]
+}
+```
+
+Notes:
+- The trigger fires a debounced re-index (2 s window) so rapid touches collapse to a single sync.
+- Triggered syncs go through the same global cross-process lock as background sync, so when multiple MCP processes share `$HOME` only one process performs the work per trigger.
+- The trigger file's *contents* are ignored — only the modification event matters.
+
+#### Background Sync Configuration (Optional)
+
+By default, the MCP server runs startup + periodic background sync for compatibility with existing installations. The global cross-process sync lock ensures only one local MCP process performs a sync cycle at a time.
+
+You can tune or disable periodic polling with environment variables:
+
+```bash
+# Default: true. Set to false to disable startup + periodic polling.
+CLAUDE_CONTEXT_BACKGROUND_SYNC=false
+
+# Optional: control how often sync runs (default: 300000 = 5 minutes)
+CLAUDE_CONTEXT_SYNC_INTERVAL_MS=60000
+```
+
+For multi-instance local stdio setups, set `CLAUDE_CONTEXT_BACKGROUND_SYNC=false` and keep the trigger watcher enabled. That avoids idle polling while still allowing external tools to request immediate re-indexing by touching `~/.context/.sync-trigger`.
+
 ## Usage with MCP Clients
 
 <details>
@@ -361,6 +407,7 @@ Pasting the following configuration into your Cursor `~/.cursor/mcp.json` file i
         "EMBEDDING_PROVIDER": "Ollama",
         "EMBEDDING_MODEL": "nomic-embed-text",
         "OLLAMA_HOST": "http://127.0.0.1:11434",
+        "EMBEDDING_DIMENSION": "768",
         "MILVUS_TOKEN": "your-zilliz-cloud-api-key"
       }
     }
@@ -471,7 +518,7 @@ Cherry Studio allows for visual MCP server configuration through its settings in
    - **Name**: `claude-context`
    - **Type**: `STDIO`
    - **Command**: `npx`
-   - **Arguments**: `["@zilliz/claude-context-mcp@latest"]`
+   - **Arguments**: `["-y", "@zilliz/claude-context-mcp@latest"]`
    - **Environment Variables**:
      - `OPENAI_API_KEY`: `your-openai-api-key`
      - `MILVUS_TOKEN`: `your-zilliz-cloud-api-key`

package/dist/config.d.ts

@@ -11,6 +11,7 @@ export interface ContextMcpConfig {
     openrouterApiKey?: string;
     ollamaModel?: string;
     ollamaHost?: string;
+    ollamaDimension?: number;
     milvusAddress?: string;
     milvusToken?: string;
     collectionNameOverride?: string;
@@ -20,7 +21,13 @@ export interface CodebaseSnapshotV1 {
     indexingCodebases: string[] | Record<string, number>;
     lastUpdated: string;
 }
-interface CodebaseInfoBase {
+export type RequestSplitterType = 'ast' | 'langchain';
+export interface CodebaseIndexOptions {
+    requestSplitter?: RequestSplitterType;
+    requestCustomExtensions?: string[];
+    requestIgnorePatterns?: string[];
+}
+interface CodebaseInfoBase extends CodebaseIndexOptions {
     lastUpdated: string;
 }
 export interface CodebaseInfoIndexing extends CodebaseInfoBase {

package/dist/config.d.ts.map

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+{"version":3,"file":"config.d.ts","sourceRoot":"","sources":["../src/config.ts"],"names":[],"mappings":"AAEA,MAAM,WAAW,gBAAgB;IAC7B,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;IAEhB,iBAAiB,EAAE,QAAQ,GAAG,UAAU,GAAG,QAAQ,GAAG,QAAQ,GAAG,YAAY,CAAC;IAC9E,cAAc,EAAE,MAAM,CAAC;IAEvB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,aAAa,CAAC,EAAE,MAAM,CAAC;IAEvB,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAE1B,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,eAAe,CAAC,EAAE,MAAM,CAAC;IAEzB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,sBAAsB,CAAC,EAAE,MAAM,CAAC;CACnC;AAGD,MAAM,WAAW,kBAAkB;IAC/B,gBAAgB,EAAE,MAAM,EAAE,CAAC;IAC3B,iBAAiB,EAAE,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACrD,WAAW,EAAE,MAAM,CAAC;CACvB;AAID,MAAM,MAAM,mBAAmB,GAAG,KAAK,GAAG,WAAW,CAAC;AAGtD,MAAM,WAAW,oBAAoB;IACjC,eAAe,CAAC,EAAE,mBAAmB,CAAC;IACtC,uBAAuB,CAAC,EAAE,MAAM,EAAE,CAAC;IACnC,qBAAqB,CAAC,EAAE,MAAM,EAAE,CAAC;CACpC;AAGD,UAAU,gBAAiB,SAAQ,oBAAoB;IACnD,WAAW,EAAE,MAAM,CAAC;CACvB;AAGD,MAAM,WAAW,oBAAqB,SAAQ,gBAAgB;IAC1D,MAAM,EAAE,UAAU,CAAC;IACnB,kBAAkB,EAAE,MAAM,CAAC;CAC9B;AAGD,MAAM,WAAW,mBAAoB,SAAQ,gBAAgB;IACzD,MAAM,EAAE,SAAS,CAAC;IAClB,YAAY,EAAE,MAAM,CAAC;IACrB,WAAW,EAAE,MAAM,CAAC;IACpB,WAAW,EAAE,WAAW,GAAG,eAAe,CAAC;CAC9C;AAGD,MAAM,WAAW,uBAAwB,SAAQ,gBAAgB;IAC7D,MAAM,EAAE,aAAa,CAAC;IACtB,YAAY,EAAE,MAAM,CAAC;IACrB,uBAAuB,CAAC,EAAE,MAAM,CAAC;CACpC;AAGD,MAAM,MAAM,YAAY,GAAG,oBAAoB,GAAG,mBAAmB,GAAG,uBAAuB,CAAC;AAEhG,MAAM,WAAW,kBAAkB;IAC/B,aAAa,EAAE,IAAI,CAAC;IACpB,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,YAAY,CAAC,CAAC;IACxC,WAAW,EAAE,MAAM,CAAC;CACvB;AAGD,MAAM,MAAM,gBAAgB,GAAG,kBAAkB,GAAG,kBAAkB,CAAC;AAGvE,wBAAgB,0BAA0B,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAenE;AAGD,wBAAgB,4BAA4B,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAiBrE;AAiBD,wBAAgB,eAAe,IAAI,gBAAgB,CAsClD;AAED,wBAAgB,uBAAuB,CAAC,MAAM,EAAE,gBAAgB,GAAG,IAAI,CA0CtE;AAED,wBAAgB,eAAe,IAAI,IAAI,CAoFtC"}

package/dist/config.js

@@ -35,11 +35,24 @@ export function getEmbeddingModelForProvider(provider) {
             return selectedModel;
     }
 }
+function getPositiveIntegerFromEnv(name) {
+    const rawValue = envManager.get(name);
+    if (!rawValue) {
+        return undefined;
+    }
+    const parsedValue = Number(rawValue);
+    if (Number.isInteger(parsedValue) && parsedValue > 0) {
+        return parsedValue;
+    }
+    console.warn(`[DEBUG] ⚠️  Ignoring invalid ${name}: ${rawValue}. Expected a positive integer.`);
+    return undefined;
+}
 export function createMcpConfig() {
     // Debug: Print all environment variables related to Context
     console.log(`[DEBUG] 🔍 Environment Variables Debug:`);
     console.log(`[DEBUG]   EMBEDDING_PROVIDER: ${envManager.get('EMBEDDING_PROVIDER') || 'NOT SET'}`);
     console.log(`[DEBUG]   EMBEDDING_MODEL: ${envManager.get('EMBEDDING_MODEL') || 'NOT SET'}`);
+    console.log(`[DEBUG]   EMBEDDING_DIMENSION: ${envManager.get('EMBEDDING_DIMENSION') || 'NOT SET'}`);
     console.log(`[DEBUG]   OLLAMA_MODEL: ${envManager.get('OLLAMA_MODEL') || 'NOT SET'}`);
     console.log(`[DEBUG]   GEMINI_API_KEY: ${envManager.get('GEMINI_API_KEY') ? 'SET (length: ' + envManager.get('GEMINI_API_KEY').length + ')' : 'NOT SET'}`);
     console.log(`[DEBUG]   OPENAI_API_KEY: ${envManager.get('OPENAI_API_KEY') ? 'SET (length: ' + envManager.get('OPENAI_API_KEY').length + ')' : 'NOT SET'}`);
@@ -63,6 +76,7 @@ export function createMcpConfig() {
         // Ollama configuration
         ollamaModel: envManager.get('OLLAMA_MODEL'),
         ollamaHost: envManager.get('OLLAMA_HOST'),
+        ollamaDimension: getPositiveIntegerFromEnv('EMBEDDING_DIMENSION'),
         // Vector database configuration - address can be auto-resolved from token
         milvusAddress: envManager.get('MILVUS_ADDRESS'), // Optional, can be resolved from token
         milvusToken: envManager.get('MILVUS_TOKEN'),
@@ -104,6 +118,9 @@ export function logConfigurationSummary(config) {
         case 'Ollama':
             console.log(`[MCP]   Ollama Host: ${config.ollamaHost || 'http://127.0.0.1:11434'}`);
             console.log(`[MCP]   Ollama Model: ${config.embeddingModel}`);
+            if (config.ollamaDimension) {
+                console.log(`[MCP]   Ollama Embedding Dimension: ${config.ollamaDimension}`);
+            }
             break;
     }
     console.log(`[MCP] 🔧 Initializing server components...`);
@@ -124,6 +141,7 @@ Environment Variables:
   Embedding Provider Configuration:
   EMBEDDING_PROVIDER      Embedding provider: OpenAI, VoyageAI, Gemini, Ollama, OpenRouter (default: OpenAI)
   EMBEDDING_MODEL         Embedding model name (works for all providers)
+  EMBEDDING_DIMENSION     Optional embedding dimension override for Ollama
   
   Provider-specific API Keys:
   OPENAI_API_KEY          OpenAI API key (required for OpenAI provider)
@@ -147,6 +165,25 @@ Environment Variables:
                           The per-codebase pathHash is preserved so multiple
                           codebases stay distinct under the same override.
 
+  MCP Sync Configuration:
+  CLAUDE_CONTEXT_BACKGROUND_SYNC
+                          Enable/disable startup + periodic background sync
+                          for indexed codebases (default: true). Set to false
+                          to disable polling while keeping trigger-based sync.
+  CLAUDE_CONTEXT_SYNC_INTERVAL_MS
+                          Background sync interval in milliseconds when enabled
+                          (default: 300000).
+
+  Sync Trigger Watcher:
+  CLAUDE_CONTEXT_TRIGGER_WATCHER
+                          Enable/disable the ~/.context/.sync-trigger filesystem
+                          watcher (default: true). When enabled, touching the
+                          trigger file kicks off an immediate, debounced re-index.
+                          Triggered syncs share the same global cross-process
+                          lock as background sync, so multi-instance setups stay
+                          coordinated. Set to false to disable filesystem
+                          watching entirely (read-only / sandboxed environments).
+
 Examples:
   # Start MCP server with OpenAI (default) and explicit Milvus address
   OPENAI_API_KEY=sk-xxx MILVUS_ADDRESS=localhost:19530 npx @zilliz/claude-context-mcp@latest
@@ -168,6 +205,9 @@ Examples:
 
   # Start MCP server with a human-readable collection name override
   OPENAI_API_KEY=sk-xxx MILVUS_TOKEN=your-token CODE_CHUNKS_COLLECTION_NAME_OVERRIDE=my_project npx @zilliz/claude-context-mcp@latest
+
+  # Start MCP server with background sync enabled every minute
+  OPENAI_API_KEY=sk-xxx MILVUS_TOKEN=your-token CLAUDE_CONTEXT_BACKGROUND_SYNC=true CLAUDE_CONTEXT_SYNC_INTERVAL_MS=60000 npx @zilliz/claude-context-mcp@latest
         `);
 }
 //# sourceMappingURL=config.js.map

package/dist/config.js.map

@@ -1 +1 @@
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package/dist/embedding.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"embedding.d.ts","sourceRoot":"","sources":["../src/embedding.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,eAAe,EAAE,iBAAiB,EAAE,eAAe,EAAE,eAAe,EAAE,MAAM,6BAA6B,CAAC;AACnH,OAAO,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAC;AAG/C,wBAAgB,uBAAuB,CAAC,MAAM,EAAE,gBAAgB,GAAG,eAAe,GAAG,iBAAiB,GAAG,eAAe,GAAG,eAAe,CA0EzI;AAED,wBAAgB,wBAAwB,CAAC,MAAM,EAAE,gBAAgB,EAAE,SAAS,EAAE,eAAe,GAAG,iBAAiB,GAAG,eAAe,GAAG,eAAe,GAAG,IAAI,CAsB3J"}
+{"version":3,"file":"embedding.d.ts","sourceRoot":"","sources":["../src/embedding.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,eAAe,EAAE,iBAAiB,EAAE,eAAe,EAAE,eAAe,EAAE,MAAM,6BAA6B,CAAC;AACnH,OAAO,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAC;AAG/C,wBAAgB,uBAAuB,CAAC,MAAM,EAAE,gBAAgB,GAAG,eAAe,GAAG,iBAAiB,GAAG,eAAe,GAAG,eAAe,CA2EzI;AAED,wBAAgB,wBAAwB,CAAC,MAAM,EAAE,gBAAgB,EAAE,SAAS,EAAE,eAAe,GAAG,iBAAiB,GAAG,eAAe,GAAG,eAAe,GAAG,IAAI,CAsB3J"}

package/dist/embedding.js

@@ -57,10 +57,11 @@ export function createEmbeddingInstance(config) {
             return openrouterEmbedding;
         case 'Ollama':
             const ollamaHost = config.ollamaHost || 'http://127.0.0.1:11434';
-            console.log(`[EMBEDDING] 🔧 Configuring Ollama with model: ${config.embeddingModel}, host: ${ollamaHost}`);
+            console.log(`[EMBEDDING] 🔧 Configuring Ollama with model: ${config.embeddingModel}, host: ${ollamaHost}${config.ollamaDimension ? `, dimension: ${config.ollamaDimension}` : ''}`);
             const ollamaEmbedding = new OllamaEmbedding({
                 model: config.embeddingModel,
-                host: ollamaHost
+                host: ollamaHost,
+                ...(config.ollamaDimension && { dimension: config.ollamaDimension })
             });
             console.log(`[EMBEDDING] ✅ Ollama embedding instance created successfully`);
             return ollamaEmbedding;
@@ -87,7 +88,7 @@ export function logEmbeddingProviderInfo(config, embedding) {
             console.log(`[EMBEDDING] OpenRouter configuration - API Key: ${config.openrouterApiKey ? '✅ Provided' : '❌ Missing'}`);
             break;
         case 'Ollama':
-            console.log(`[EMBEDDING] Ollama configuration - Host: ${config.ollamaHost || 'http://127.0.0.1:11434'}, Model: ${config.embeddingModel}`);
+            console.log(`[EMBEDDING] Ollama configuration - Host: ${config.ollamaHost || 'http://127.0.0.1:11434'}, Model: ${config.embeddingModel}${config.ollamaDimension ? `, Dimension: ${config.ollamaDimension}` : ''}`);
             break;
     }
 }

package/dist/embedding.js.map

@@ -1 +1 @@
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+{"version":3,"file":"embedding.js","sourceRoot":"","sources":["../src/embedding.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,eAAe,EAAE,iBAAiB,EAAE,eAAe,EAAE,eAAe,EAAE,MAAM,6BAA6B,CAAC;AAGnH,iEAAiE;AACjE,MAAM,UAAU,uBAAuB,CAAC,MAAwB;IAC5D,OAAO,CAAC,GAAG,CAAC,wBAAwB,MAAM,CAAC,iBAAiB,wBAAwB,CAAC,CAAC;IAEtF,QAAQ,MAAM,CAAC,iBAAiB,EAAE,CAAC;QAC/B,KAAK,QAAQ;YACT,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAC;gBACvB,OAAO,CAAC,KAAK,CAAC,2DAA2D,CAAC,CAAC;gBAC3E,MAAM,IAAI,KAAK,CAAC,0DAA0D,CAAC,CAAC;YAChF,CAAC;YACD,OAAO,CAAC,GAAG,CAAC,iDAAiD,MAAM,CAAC,cAAc,EAAE,CAAC,CAAC;YACtF,MAAM,eAAe,GAAG,IAAI,eAAe,CAAC;gBACxC,MAAM,EAAE,MAAM,CAAC,YAAY;gBAC3B,KAAK,EAAE,MAAM,CAAC,cAAc;gBAC5B,GAAG,CAAC,MAAM,CAAC,aAAa,IAAI,EAAE,OAAO,EAAE,MAAM,CAAC,aAAa,EAAE,CAAC;aACjE,CAAC,CAAC;YACH,OAAO,CAAC,GAAG,CAAC,8DAA8D,CAAC,CAAC;YAC5E,OAAO,eAAe,CAAC;QAE3B,KAAK,UAAU;YACX,IAAI,CAAC,MAAM,CAAC,cAAc,EAAE,CAAC;gBACzB,OAAO,CAAC,KAAK,CAAC,6DAA6D,CAAC,CAAC;gBAC7E,MAAM,IAAI,KAAK,CAAC,8DAA8D,CAAC,CAAC;YACpF,CAAC;YACD,OAAO,CAAC,GAAG,CAAC,mDAAmD,MAAM,CAAC,cAAc,EAAE,CAAC,CAAC;YACxF,MAAM,eAAe,GAAG,IAAI,iBAAiB,CAAC;gBAC1C,MAAM,EAAE,MAAM,CAAC,cAAc;gBAC7B,KAAK,EAAE,MAAM,CAAC,cAAc;aAC/B,CAAC,CAAC;YACH,OAAO,CAAC,GAAG,CAAC,gEAAgE,CAAC,CAAC;YAC9E,OAAO,eAAe,CAAC;QAE3B,KAAK,QAAQ;YACT,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAC;gBACvB,OAAO,CAAC,KAAK,CAAC,2DAA2D,CAAC,CAAC;gBAC3E,MAAM,IAAI,KAAK,CAAC,0DAA0D,CAAC,CAAC;YAChF,CAAC;YACD,OAAO,CAAC,GAAG,CAAC,iDAAiD,MAAM,CAAC,cAAc,EAAE,CAAC,CAAC;YACtF,MAAM,eAAe,GAAG,IAAI,eAAe,CAAC;gBACxC,MAAM,EAAE,MAAM,CAAC,YAAY;gBAC3B,KAAK,EAAE,MAAM,CAAC,cAAc;gBAC5B,GAAG,CAAC,MAAM,CAAC,aAAa,IAAI,EAAE,OAAO,EAAE,MAAM,CAAC,aAAa,EAAE,CAAC;aACjE,CAAC,CAAC;YACH,OAAO,CAAC,GAAG,CAAC,8DAA8D,CAAC,CAAC;YAC5E,OAAO,eAAe,CAAC;QAE3B,KAAK,YAAY;YACb,IAAI,CAAC,MAAM,CAAC,gBAAgB,EAAE,CAAC;gBAC3B,OAAO,CAAC,KAAK,CAAC,+DAA+D,CAAC,CAAC;gBAC/E,MAAM,IAAI,KAAK,CAAC,kEAAkE,CAAC,CAAC;YACxF,CAAC;YACD,OAAO,CAAC,GAAG,CAAC,qDAAqD,MAAM,CAAC,cAAc,EAAE,CAAC,CAAC;YAC1F,qEAAqE;YACrE,MAAM,mBAAmB,GAAG,IAAI,eAAe,CAAC;gBAC5C,MAAM,EAAE,MAAM,CAAC,gBAAgB;gBAC/B,KAAK,EAAE,MAAM,CAAC,cAAc;gBAC5B,OAAO,EAAE,8BAA8B;aAC1C,CAAC,CAAC;YACH,OAAO,CAAC,GAAG,CAAC,kEAAkE,CAAC,CAAC;YAChF,OAAO,mBAAmB,CAAC;QAE/B,KAAK,QAAQ;YACT,MAAM,UAAU,GAAG,MAAM,CAAC,UAAU,IAAI,wBAAwB,CAAC;YACjE,OAAO,CAAC,GAAG,CAAC,iDAAiD,MAAM,CAAC,cAAc,WAAW,UAAU,GAAG,MAAM,CAAC,eAAe,CAAC,CAAC,CAAC,gBAAgB,MAAM,CAAC,eAAe,EAAE,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACpL,MAAM,eAAe,GAAG,IAAI,eAAe,CAAC;gBACxC,KAAK,EAAE,MAAM,CAAC,cAAc;gBAC5B,IAAI,EAAE,UAAU;gBAChB,GAAG,CAAC,MAAM,CAAC,eAAe,IAAI,EAAE,SAAS,EAAE,MAAM,CAAC,eAAe,EAAE,CAAC;aACvE,CAAC,CAAC;YACH,OAAO,CAAC,GAAG,CAAC,8DAA8D,CAAC,CAAC;YAC5E,OAAO,eAAe,CAAC;QAE3B;YACI,OAAO,CAAC,KAAK,CAAC,iDAAiD,MAAM,CAAC,iBAAiB,EAAE,CAAC,CAAC;YAC3F,MAAM,IAAI,KAAK,CAAC,mCAAmC,MAAM,CAAC,iBAAiB,EAAE,CAAC,CAAC;IACvF,CAAC;AACL,CAAC;AAED,MAAM,UAAU,wBAAwB,CAAC,MAAwB,EAAE,SAAkF;IACjJ,OAAO,CAAC,GAAG,CAAC,0CAA0C,MAAM,CAAC,iBAAiB,qBAAqB,CAAC,CAAC;IACrG,OAAO,CAAC,GAAG,CAAC,yCAAyC,MAAM,CAAC,cAAc,gBAAgB,SAAS,CAAC,YAAY,EAAE,EAAE,CAAC,CAAC;IAEtH,8CAA8C;IAC9C,QAAQ,MAAM,CAAC,iBAAiB,EAAE,CAAC;QAC/B,KAAK,QAAQ;YACT,OAAO,CAAC,GAAG,CAAC,+CAA+C,MAAM,CAAC,YAAY,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,WAAW,eAAe,MAAM,CAAC,aAAa,IAAI,SAAS,EAAE,CAAC,CAAC;YAC/J,MAAM;QACV,KAAK,UAAU;YACX,OAAO,CAAC,GAAG,CAAC,iDAAiD,MAAM,CAAC,cAAc,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC;YACnH,MAAM;QACV,KAAK,QAAQ;YACT,OAAO,CAAC,GAAG,CAAC,+CAA+C,MAAM,CAAC,YAAY,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,WAAW,eAAe,MAAM,CAAC,aAAa,IAAI,SAAS,EAAE,CAAC,CAAC;YAC/J,MAAM;QACV,KAAK,YAAY;YACb,OAAO,CAAC,GAAG,CAAC,mDAAmD,MAAM,CAAC,gBAAgB,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC;YACvH,MAAM;QACV,KAAK,QAAQ;YACT,OAAO,CAAC,GAAG,CAAC,4CAA4C,MAAM,CAAC,UAAU,IAAI,wBAAwB,YAAY,MAAM,CAAC,cAAc,GAAG,MAAM,CAAC,eAAe,CAAC,CAAC,CAAC,gBAAgB,MAAM,CAAC,eAAe,EAAE,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACnN,MAAM;IACd,CAAC;AACL,CAAC"}

package/dist/handlers.d.ts

@@ -5,6 +5,14 @@ export declare class ToolHandlers {
     private snapshotManager;
     private indexingStats;
     private currentWorkspace;
+    /**
+     * Tracks active background indexing tasks per absolute codebase path so
+     * clear_index can cancel and await them before dropping the collection.
+     * Without this, a clear_index call returns "successfully cleared" while
+     * the background task keeps embedding chunks and writing them into the
+     * just-cleared collection (issue #199).
+     */
+    private indexingTasks;
     constructor(context: Context, snapshotManager: SnapshotManager);
     /**
      * Query Milvus for the real row count of a codebase's collection.

package/dist/handlers.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"handlers.d.ts","sourceRoot":"","sources":["../src/handlers.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,OAAO,EAA4B,MAAM,6BAA6B,CAAC;AAChF,OAAO,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAGhD,qBAAa,YAAY;IACrB,OAAO,CAAC,OAAO,CAAU;IACzB,OAAO,CAAC,eAAe,CAAkB;IACzC,OAAO,CAAC,aAAa,CAA8D;IACnF,OAAO,CAAC,gBAAgB,CAAS;gBAErB,OAAO,EAAE,OAAO,EAAE,eAAe,EAAE,eAAe;IAO9D;;;;;;;OAOG;YACW,oBAAoB;IAuBlC;;;;;;;;OAQG;IACU,yBAAyB,IAAI,OAAO,CAAC,IAAI,CAAC;IAqFvD;;;;;;;;;;OAUG;YACW,6BAA6B;IAsJ9B,mBAAmB,CAAC,IAAI,EAAE,GAAG;;;;;;;;;;;;;YAoM5B,uBAAuB;IA2FxB,gBAAgB,CAAC,IAAI,EAAE,GAAG;;;;;;;;;;;;;IA+M1B,gBAAgB,CAAC,IAAI,EAAE,GAAG;;;;;;;;;;;;;IAwH1B,uBAAuB,CAAC,IAAI,EAAE,GAAG;;;;;;;;;;;;;CAmHjD"}
+{"version":3,"file":"handlers.d.ts","sourceRoot":"","sources":["../src/handlers.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,OAAO,EAA+D,MAAM,6BAA6B,CAAC;AACnH,OAAO,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAKhD,qBAAa,YAAY;IACrB,OAAO,CAAC,OAAO,CAAU;IACzB,OAAO,CAAC,eAAe,CAAkB;IACzC,OAAO,CAAC,aAAa,CAA8D;IACnF,OAAO,CAAC,gBAAgB,CAAS;IACjC;;;;;;OAMG;IACH,OAAO,CAAC,aAAa,CAAmF;gBAE5F,OAAO,EAAE,OAAO,EAAE,eAAe,EAAE,eAAe;IAO9D;;;;;;;OAOG;YACW,oBAAoB;IAuBlC;;;;;;;;OAQG;IACU,yBAAyB,IAAI,OAAO,CAAC,IAAI,CAAC;IAqFvD;;;;;;;;;;OAUG;YACW,6BAA6B;IA6J9B,mBAAmB,CAAC,IAAI,EAAE,GAAG;;;;;;;;;;;;;YA2N5B,uBAAuB;IAwGxB,gBAAgB,CAAC,IAAI,EAAE,GAAG;;;;;;;;;;;;;IA+M1B,gBAAgB,CAAC,IAAI,EAAE,GAAG;;;;;;;;;;;;;IA0I1B,uBAAuB,CAAC,IAAI,EAAE,GAAG;;;;;;;;;;;;;CAmHjD"}

package/dist/handlers.js

@@ -1,10 +1,19 @@
 import * as fs from "fs";
 import * as path from "path";
-import { COLLECTION_LIMIT_MESSAGE } from "@zilliz/claude-context-core";
+import { COLLECTION_LIMIT_MESSAGE, FileSynchronizer, IndexAbortError } from "@zilliz/claude-context-core";
+import { createRequestSplitter, isRequestSplitterType } from "./splitter.js";
 import { ensureAbsolutePath, truncateContent, trackCodebasePath } from "./utils.js";
 export class ToolHandlers {
     constructor(context, snapshotManager) {
         this.indexingStats = null;
+        /**
+         * Tracks active background indexing tasks per absolute codebase path so
+         * clear_index can cancel and await them before dropping the collection.
+         * Without this, a clear_index call returns "successfully cleared" while
+         * the background task keeps embedding chunks and writing them into the
+         * just-cleared collection (issue #199).
+         */
+        this.indexingTasks = new Map();
         this.context = context;
         this.snapshotManager = snapshotManager;
         this.currentWorkspace = process.cwd();
@@ -245,6 +254,12 @@ export class ToolHandlers {
                 if (!cloudCodebases.has(localCodebase)) {
                     this.snapshotManager.removeCodebaseCompletely(localCodebase);
                     hasChanges = true;
+                    try {
+                        await FileSynchronizer.deleteSnapshot(localCodebase);
+                    }
+                    catch (error) {
+                        console.warn(`[SYNC-CLOUD] ⚠️  Failed to delete local merkle snapshot for removed codebase '${localCodebase}':`, error?.message || error);
+                    }
                     console.log(`[SYNC-CLOUD] ➖ Removed local codebase (not in cloud): ${localCodebase}`);
                 }
             }
@@ -284,22 +299,28 @@ export class ToolHandlers {
     async handleIndexCodebase(args) {
         const { path: codebasePath, force, splitter, customExtensions, ignorePatterns } = args;
         const forceReindex = force || false;
-        const splitterType = splitter || 'ast'; // Default to AST
+        const requestedSplitter = splitter || 'ast'; // Default to AST
         const customFileExtensions = customExtensions || [];
         const customIgnorePatterns = ignorePatterns || [];
         try {
             // Sync indexed codebases from cloud first
             await this.syncIndexedCodebasesFromCloud();
             // Validate splitter parameter
-            if (splitterType !== 'ast' && splitterType !== 'langchain') {
+            if (!isRequestSplitterType(requestedSplitter)) {
                 return {
                     content: [{
                             type: "text",
-                            text: `Error: Invalid splitter type '${splitterType}'. Must be 'ast' or 'langchain'.`
+                            text: `Error: Invalid splitter type '${requestedSplitter}'. Must be 'ast' or 'langchain'.`
                         }],
                     isError: true
                 };
             }
+            const splitterType = requestedSplitter;
+            const indexOptions = {
+                requestSplitter: splitterType,
+                requestCustomExtensions: customFileExtensions,
+                requestIgnorePatterns: customIgnorePatterns
+            };
             // Force absolute path resolution - warn if relative path provided
             const absolutePath = ensureAbsolutePath(codebasePath);
             // Validate path exists
@@ -411,10 +432,8 @@ export class ToolHandlers {
                     isError: true
                 };
             }
-            // Add custom extensions if provided
             if (customFileExtensions.length > 0) {
-                console.log(`[CUSTOM-EXTENSIONS] Adding ${customFileExtensions.length} custom extensions: ${customFileExtensions.join(', ')}`);
-                this.context.addCustomExtensions(customFileExtensions);
+                console.log(`[CUSTOM-EXTENSIONS] Using ${customFileExtensions.length} request-scoped custom extensions: ${customFileExtensions.join(', ')}`);
             }
             // Check current status and log if retrying after failure
             const currentStatus = this.snapshotManager.getCodebaseStatus(absolutePath);
@@ -423,12 +442,23 @@ export class ToolHandlers {
                 console.log(`[BACKGROUND-INDEX] Retrying indexing for previously failed codebase. Previous error: ${failedInfo?.errorMessage || 'Unknown error'}`);
             }
             // Set to indexing status and save snapshot immediately
-            this.snapshotManager.setCodebaseIndexing(absolutePath, 0);
+            this.snapshotManager.setCodebaseIndexing(absolutePath, 0, indexOptions);
             this.snapshotManager.saveCodebaseSnapshot();
             // Track the codebase path for syncing
             trackCodebasePath(absolutePath);
-            // Start background indexing - now safe to proceed
-            this.startBackgroundIndexing(absolutePath, forceReindex, splitterType, customIgnorePatterns);
+            // Start background indexing - now safe to proceed.
+            // Track the controller + promise so clear_index can cancel and
+            // await us before dropping the underlying collection.
+            const controller = new AbortController();
+            const promise = this.startBackgroundIndexing(absolutePath, forceReindex, splitterType, customIgnorePatterns, customFileExtensions, indexOptions, controller.signal).finally(() => {
+                // Only clear the entry if it still points at this run — a
+                // concurrent re-index may have replaced us.
+                const current = this.indexingTasks.get(absolutePath);
+                if (current && current.controller === controller) {
+                    this.indexingTasks.delete(absolutePath);
+                }
+            });
+            this.indexingTasks.set(absolutePath, { controller, promise });
             const pathInfo = codebasePath !== absolutePath
                 ? `\nNote: Input path '${codebasePath}' was resolved to absolute path '${absolutePath}'`
                 : '';
@@ -458,7 +488,7 @@ export class ToolHandlers {
             };
         }
     }
-    async startBackgroundIndexing(codebasePath, forceReindex, splitterType, customIgnorePatterns = []) {
+    async startBackgroundIndexing(codebasePath, forceReindex, splitterType, customIgnorePatterns = [], customFileExtensions = [], indexOptions, signal) {
         const absolutePath = codebasePath;
         let lastSaveTime = 0; // Track last save timestamp
         try {
@@ -467,34 +497,30 @@ export class ToolHandlers {
             if (forceReindex) {
                 console.log(`[BACKGROUND-INDEX] ℹ️  Force reindex mode - collection was already cleared during validation`);
             }
-            // Use the existing Context instance for indexing.
-            let contextForThisTask = this.context;
-            if (splitterType !== 'ast') {
-                console.warn(`[BACKGROUND-INDEX] Non-AST splitter '${splitterType}' requested; falling back to AST splitter`);
-            }
+            const requestSplitter = createRequestSplitter(splitterType);
             // Load ignore patterns from files first (including .ignore, .gitignore, etc.)
             // and merge them with this request's custom ignore patterns without
             // relying on shared Context state for this background indexing task.
             const ignorePatterns = await this.context.getEffectiveIgnorePatterns(absolutePath, customIgnorePatterns);
+            const supportedExtensions = this.context.getEffectiveSupportedExtensions(customFileExtensions);
             // Initialize file synchronizer with proper ignore patterns (including project-specific patterns)
-            const { FileSynchronizer } = await import("@zilliz/claude-context-core");
             console.log(`[BACKGROUND-INDEX] Using ignore patterns: ${ignorePatterns.join(', ')}`);
-            const synchronizer = new FileSynchronizer(absolutePath, ignorePatterns, this.context.getSupportedExtensions());
+            if (customFileExtensions.length > 0) {
+                console.log(`[BACKGROUND-INDEX] Using ${customFileExtensions.length} request-scoped custom extensions: ${customFileExtensions.join(', ')}`);
+            }
+            const synchronizer = new FileSynchronizer(absolutePath, ignorePatterns, supportedExtensions);
             await synchronizer.initialize();
             // Store synchronizer in the context (let context manage collection names)
             await this.context.getPreparedCollection(absolutePath);
             const collectionName = this.context.getCollectionName(absolutePath);
             this.context.setSynchronizer(collectionName, synchronizer);
-            if (contextForThisTask !== this.context) {
-                contextForThisTask.setSynchronizer(collectionName, synchronizer);
-            }
             console.log(`[BACKGROUND-INDEX] Starting indexing with ${splitterType} splitter for: ${absolutePath}`);
             // Log embedding provider information before indexing
             const embeddingProvider = this.context.getEmbedding();
             console.log(`[BACKGROUND-INDEX] 🧠 Using embedding provider: ${embeddingProvider.getProvider()} with dimension: ${embeddingProvider.getDimension()}`);
             // Start indexing with the appropriate context and progress tracking
             console.log(`[BACKGROUND-INDEX] 🚀 Beginning codebase indexing process...`);
-            const stats = await contextForThisTask.indexCodebase(absolutePath, (progress) => {
+            const stats = await this.context.indexCodebase(absolutePath, (progress) => {
                 // Update progress in snapshot manager using new method
                 this.snapshotManager.setCodebaseIndexing(absolutePath, progress.percentage);
                 // Save snapshot periodically (every 2 seconds to avoid too frequent saves)
@@ -505,10 +531,10 @@ export class ToolHandlers {
                     console.log(`[BACKGROUND-INDEX] 💾 Saved progress snapshot at ${progress.percentage.toFixed(1)}%`);
                 }
                 console.log(`[BACKGROUND-INDEX] Progress: ${progress.phase} - ${progress.percentage}% (${progress.current}/${progress.total})`);
-            }, false, customIgnorePatterns);
+            }, false, customIgnorePatterns, customFileExtensions, requestSplitter, signal);
             console.log(`[BACKGROUND-INDEX] ✅ Indexing completed successfully! Files: ${stats.indexedFiles}, Chunks: ${stats.totalChunks}`);
             // Set codebase to indexed status with complete statistics
-            this.snapshotManager.setCodebaseIndexed(absolutePath, stats);
+            this.snapshotManager.setCodebaseIndexed(absolutePath, stats, indexOptions);
             this.indexingStats = { indexedFiles: stats.indexedFiles, totalChunks: stats.totalChunks };
             // Save snapshot after updating codebase lists
             this.snapshotManager.saveCodebaseSnapshot();
@@ -519,12 +545,20 @@ export class ToolHandlers {
             console.log(`[BACKGROUND-INDEX] ${message}`);
         }
         catch (error) {
+            // Cooperative cancel from clear_index — clear_index is responsible
+            // for tearing down the snapshot/collection right after, so do not
+            // overwrite the snapshot with an "indexfailed" entry that would
+            // race the clear and leave a tombstone behind.
+            if (error instanceof IndexAbortError) {
+                console.log(`[BACKGROUND-INDEX] Indexing for ${absolutePath} was cancelled: ${error.message}`);
+                return;
+            }
             console.error(`[BACKGROUND-INDEX] Error during indexing for ${absolutePath}:`, error);
             // Get the last attempted progress
             const lastProgress = this.snapshotManager.getIndexingProgress(absolutePath);
             // Set codebase to failed status with error information
             const errorMessage = error.message || String(error);
-            this.snapshotManager.setCodebaseIndexFailed(absolutePath, errorMessage, lastProgress);
+            this.snapshotManager.setCodebaseIndexFailed(absolutePath, errorMessage, lastProgress, indexOptions);
             this.snapshotManager.saveCodebaseSnapshot();
             // Log error but don't crash MCP service - indexing errors are handled gracefully
             console.error(`[BACKGROUND-INDEX] Indexing failed for ${absolutePath}: ${errorMessage}`);
@@ -758,6 +792,24 @@ export class ToolHandlers {
                 };
             }
             console.log(`[CLEAR] Clearing codebase: ${absolutePath}`);
+            // Cancel any in-flight background indexing for this codebase and
+            // wait for it to wind down before we drop the collection.
+            // Otherwise the background task keeps embedding chunks and writes
+            // them into the just-cleared collection (issue #199).
+            const activeTask = this.indexingTasks.get(absolutePath);
+            if (activeTask) {
+                console.log(`[CLEAR] Cancelling in-flight background indexing for: ${absolutePath}`);
+                activeTask.controller.abort();
+                try {
+                    await activeTask.promise;
+                }
+                catch (waitError) {
+                    // startBackgroundIndexing already logs and never re-throws,
+                    // so this catch only guards against future refactors.
+                    console.warn(`[CLEAR] Background indexing wind-down reported: ${waitError?.message || waitError}`);
+                }
+                this.indexingTasks.delete(absolutePath);
+            }
             try {
                 await this.context.clearIndex(absolutePath);
                 console.log(`[CLEAR] Successfully cleared index for: ${absolutePath}`);