fix: resolve orphaned subprocesses and Chroma HTTP regressions

- Add subprocess cleanup after SDK query loop completes, using existing
  ProcessRegistry infrastructure (getProcessBySession + ensureProcessExit)
- Replace npx-based Chroma binary spawning with absolute path resolution
  via require.resolve, falling back to npx with explicit cwd (#1120)
- Remove @chroma-core/default-embed client-side dependency; let Chroma
  HTTP server handle embeddings server-side (#1104, #1105, #1110)

Closes #1010, #1089, #1090, #1068, #1120, #1104, #1105, #1110

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

src/services/sync/ChromaServerManager.ts

@@ -11,7 +11,7 @@
 import { spawn, ChildProcess, execSync } from 'child_process';
 import path from 'path';
 import os from 'os';
-import fs from 'fs';
+import fs, { existsSync } from 'fs';
 import { logger } from '../../utils/logger.js';
 
 export interface ChromaServerConfig {
@@ -108,14 +108,34 @@ export class ChromaServerManager {
 
     // Cross-platform: use npx.cmd on Windows
     const isWindows = process.platform === 'win32';
-    const command = isWindows ? 'npx.cmd' : 'npx';
 
-    const args = [
-      'chroma', 'run',
-      '--path', this.config.dataDir,
-      '--host', this.config.host,
-      '--port', String(this.config.port)
-    ];
+    // Resolve chroma binary absolutely — npx fails when spawned from cache dirs (#1120)
+    let command: string;
+    let args: string[];
+    try {
+      // chromadb package installs a 'chroma' bin entry
+      const chromaBinDir = path.dirname(require.resolve('chromadb/package.json'));
+      const chromaBin = path.join(chromaBinDir, 'node_modules', '.bin', isWindows ? 'chroma.cmd' : 'chroma');
+      // Fallback: check project-level .bin
+      const projectBin = path.join(chromaBinDir, '..', '.bin', isWindows ? 'chroma.cmd' : 'chroma');
+
+      if (existsSync(chromaBin)) {
+        command = chromaBin;
+      } else if (existsSync(projectBin)) {
+        command = projectBin;
+      } else {
+        // Last resort: npx with explicit cwd
+        command = isWindows ? 'npx.cmd' : 'npx';
+      }
+    } catch {
+      command = isWindows ? 'npx.cmd' : 'npx';
+    }
+
+    if (command.includes('npx')) {
+      args = ['chroma', 'run', '--path', this.config.dataDir, '--host', this.config.host, '--port', String(this.config.port)];
+    } else {
+      args = ['run', '--path', this.config.dataDir, '--host', this.config.host, '--port', String(this.config.port)];
+    }
 
     logger.info('CHROMA_SERVER', 'Starting Chroma server', {
       command,
@@ -125,11 +145,20 @@ export class ChromaServerManager {
 
     const spawnEnv = this.getSpawnEnv();
 
+    // Resolve cwd for npx fallback — ensures node_modules is findable (#1120)
+    let spawnCwd: string | undefined;
+    try {
+      spawnCwd = path.dirname(require.resolve('chromadb/package.json'));
+    } catch {
+      // If chromadb isn't resolvable, omit cwd and let npx handle it
+    }
+
     this.serverProcess = spawn(command, args, {
       stdio: ['ignore', 'pipe', 'pipe'],
       detached: !isWindows,  // Don't detach on Windows (no process groups)
       windowsHide: true,     // Hide console window on Windows
-      env: spawnEnv
+      env: spawnEnv,
+      ...(spawnCwd && { cwd: spawnCwd })
     });
 
     // Log server output for debugging

src/services/sync/ChromaSync.ts

@@ -189,14 +189,11 @@ export class ChromaSync {
     }
 
     try {
-      // getOrCreateCollection handles both cases
-      // Lazy-load DefaultEmbeddingFunction to avoid eagerly pulling in
-      // @huggingface/transformers → sharp native binaries at bundle startup
-      const { DefaultEmbeddingFunction } = await import('@chroma-core/default-embed');
-      const embeddingFunction = new DefaultEmbeddingFunction();
+      // Let the Chroma HTTP server handle embeddings server-side.
+      // Removes dependency on @chroma-core/default-embed which requires
+      // onnxruntime + sharp native binaries that fail on many platforms (#1104, #1105, #1110).
       this.collection = await this.chromaClient.getOrCreateCollection({
-        name: this.collectionName,
-        embeddingFunction
+        name: this.collectionName
       });
 
       logger.debug('CHROMA_SYNC', 'Collection ready', { collection: this.collectionName });

src/services/worker/SDKAgent.ts

@@ -272,6 +272,12 @@ export class SDKAgent {
       }
     }
 
+    // Ensure subprocess is terminated after query completes
+    const tracked = getProcessBySession(session.sessionDbId);
+    if (tracked && !tracked.process.killed && tracked.process.exitCode === null) {
+      await ensureProcessExit(tracked, 5000);
+    }
+
     // Mark session complete
     const sessionDuration = Date.now() - session.startTime;
     logger.success('SDK', 'Agent completed', {