Remove SQLite/Drizzle infrastructure from dev branch

Strip all database dependencies and revert to main's file-backed stores:
- Delete packages/server/src/server/db/ (schema, migrations, DB stores, legacy importers)
- Remove better-sqlite3, drizzle-orm, drizzle-kit, @electron/rebuild deps
- Revert bootstrap.ts to FileBackedProjectRegistry/WorkspaceRegistry/AgentStorage
- Restore workspace-registry-bootstrap.ts from main
- Revert AgentSnapshotStore → AgentStorage across all files
- Fix session.ts field names (directory→cwd, numeric id→string workspaceId)
- Remove DB-only tests from bootstrap.smoke.test, agent-manager.test, etc.

packages/server/package.json

@@ -31,7 +31,7 @@
     "dev": "cross-env NODE_ENV=development tsx scripts/dev-runner.ts",
     "dev:tsx": "cross-env NODE_ENV=development tsx watch --ignore '**/*.timestamp-*' src/server/index.ts",
     "build": "node -e \"require('node:fs').rmSync('dist',{ recursive: true, force: true })\" && npm run build:lib && npm run build:scripts",
-    "build:lib": "tsc -p tsconfig.server.json --incremental false && node -e \"const fs=require('node:fs'); fs.mkdirSync('dist/server/server/speech/providers/local/sherpa/assets',{recursive:true}); fs.copyFileSync('src/server/speech/providers/local/sherpa/assets/silero_vad.onnx','dist/server/server/speech/providers/local/sherpa/assets/silero_vad.onnx'); fs.cpSync('src/terminal/shell-integration','dist/server/terminal/shell-integration',{recursive:true}); fs.cpSync('src/terminal/shell-integration','dist/src/terminal/shell-integration',{recursive:true}); fs.cpSync('src/server/db/migrations','dist/server/server/db/migrations',{recursive:true});\"",
+    "build:lib": "tsc -p tsconfig.server.json --incremental false && node -e \"const fs=require('node:fs'); fs.mkdirSync('dist/server/server/speech/providers/local/sherpa/assets',{recursive:true}); fs.copyFileSync('src/server/speech/providers/local/sherpa/assets/silero_vad.onnx','dist/server/server/speech/providers/local/sherpa/assets/silero_vad.onnx'); fs.cpSync('src/terminal/shell-integration','dist/server/terminal/shell-integration',{recursive:true}); fs.cpSync('src/terminal/shell-integration','dist/src/terminal/shell-integration',{recursive:true});\"",
     "build:scripts": "tsc -p tsconfig.scripts.json --incremental false && node -e \"const fs=require('node:fs'); fs.mkdirSync('dist/scripts',{recursive:true}); fs.copyFileSync('scripts/mcp-stdio-socket-bridge-cli.mjs','dist/scripts/mcp-stdio-socket-bridge-cli.mjs');\"",
     "prepack": "npm run build",
     "start": "cross-env NODE_ENV=production node dist/server/server/index.js",
@@ -41,7 +41,6 @@
     "speech:download": "tsx scripts/download-speech-models.ts",
     "speech:tts:matrix": "tsx scripts/generate-sherpa-tts-matrix.ts",
     "speech:transcribe:local": "tsx scripts/transcribe-local-wav.ts",
-    "db:query": "tsx scripts/db-query.ts",
     "test": "npm run test:unit && npm run test:integration",
     "test:unit": "vitest run --exclude \"**/*.e2e.test.ts\"",
     "test:integration": "vitest run --maxWorkers=1 --minWorkers=1 src/server/daemon-e2e/models.e2e.test.ts src/server/daemon-e2e/live-preferences.e2e.test.ts src/server/agent/model-catalog.e2e.test.ts",
@@ -71,8 +70,6 @@
     "ai": "5.0.78",
     "ajv": "^8.17.1",
     "dotenv": "^17.2.3",
-    "better-sqlite3": "^12.8.0",
-    "drizzle-orm": "^0.45.1",
     "express": "^4.18.2",
     "express-basic-auth": "^1.2.1",
     "fast-deep-equal": "^3.1.3",
@@ -98,8 +95,6 @@
   },
   "devDependencies": {
     "@playwright/test": "^1.56.1",
-    "@types/better-sqlite3": "^7.6.13",
-    "drizzle-kit": "^0.31.10",
     "@types/express": "^4.17.20",
     "@types/node": "^20.9.0",
     "@types/qrcode": "^1.5.6",