feat: replace WASM embeddings with persistent chroma-mcp MCP connection (#1176)

* feat: replace WASM embeddings with persistent chroma-mcp MCP connection

Replace ChromaServerManager (npx chroma run + chromadb npm + ONNX/WASM)
with ChromaMcpManager, a singleton stdio MCP client that communicates with
chroma-mcp via uvx. This eliminates native binary issues, segfaults, and
WASM embedding failures that plagued cross-platform installs.

Key changes:
- Add ChromaMcpManager: singleton MCP client with lazy connect, auto-reconnect,
  connection lock, and Zscaler SSL cert support
- Rewrite ChromaSync to use MCP tool calls instead of chromadb npm client
- Handle chroma-mcp's non-JSON responses (plain text success/error messages)
- Treat "collection already exists" as idempotent success
- Wire ChromaMcpManager into GracefulShutdown for clean subprocess teardown
- Delete ChromaServerManager (no longer needed)

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

* fix: address PR review — connection guard leak, timer leak, async reset

- Clear connecting guard in finally block to prevent permanent reconnection block
- Clear timeout after successful connection to prevent timer leak
- Make reset() async to await stop() before nullifying instance
- Delete obsolete chroma-server-manager test (imports deleted class)
- Update graceful-shutdown test to use chromaMcpManager property name

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

* fix: prevent chroma-mcp spawn storm — zombie cleanup, stale onclose guard, reconnect backoff

Three bugs caused chroma-mcp processes to accumulate (92+ observed):

1. Zombie on timeout: failed connections left subprocess alive because
   only the timer was cleared, not the transport. Now catch block
   explicitly closes transport+client before rethrowing.

2. Stale onclose race: old transport's onclose handler captured `this`
   and overwrote the current connection reference after reconnect,
   orphaning the new subprocess. Now guarded with reference check.

3. No backoff: every failure triggered immediate reconnect. With
   backfill doing hundreds of MCP calls, this created rapid-fire
   spawning. Added 10s backoff on both connection failure and
   unexpected process death.

Also includes ChromaSync fixes from PR review:
- queryChroma deduplication now preserves index-aligned arrays
- SQL injection guard on backfill ID exclusion lists

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

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

src/shared/SettingsDefaultsManager.ts

@@ -118,7 +118,7 @@ export class SettingsDefaultsManager {
     CLAUDE_MEM_EXCLUDED_PROJECTS: '',  // Comma-separated glob patterns for excluded project paths
     CLAUDE_MEM_FOLDER_MD_EXCLUDE: '[]',  // JSON array of folder paths to exclude from CLAUDE.md generation
     // Chroma Vector Database Configuration
-    CLAUDE_MEM_CHROMA_MODE: 'local',           // 'local' starts npx chroma run, 'remote' connects to existing server
+    CLAUDE_MEM_CHROMA_MODE: 'local',           // 'local' uses persistent chroma-mcp via uvx, 'remote' connects to existing server
     CLAUDE_MEM_CHROMA_HOST: '127.0.0.1',
     CLAUDE_MEM_CHROMA_PORT: '8000',
     CLAUDE_MEM_CHROMA_SSL: 'false',