feat: Replace SQLite with JSON logging for macOS sandbox compatibility

- Removes the sqlite3 dependency and refactors the logging mechanism to use a JSON file (logs.json) instead of a database.
- This change is a temporary workaround to address issues with macOS sandboxing that were caused by the SQLite native module.
- Storing all logs in a single JSON file may introduce scalability concerns in the future.

Fixes https://github.com/google-gemini/gemini-cli/issues/522

package.json

@@ -24,7 +24,7 @@
     "auth:docker": "gcloud auth configure-docker us-west1-docker.pkg.dev",
     "auth": "npm run auth:npm && npm run auth:docker",
     "prerelease:dev": "npm run prerelease:version --workspaces && npm run prerelease:deps --workspaces",
-    "bundle": "node_modules/.bin/esbuild packages/cli/index.ts --bundle --outfile=bundle/gemini.js --platform=node --format=esm --external:sqlite3 --banner:js=\"import { createRequire } from 'module'; const require = createRequire(import.meta.url); globalThis.__filename = require('url').fileURLToPath(import.meta.url); globalThis.__dirname = require('path').dirname(globalThis.__filename);\" && bash scripts/copy_bundle_assets.sh"
+    "bundle": "node_modules/.bin/esbuild packages/cli/index.ts --bundle --outfile=bundle/gemini.js --platform=node --format=esm --banner:js=\"import { createRequire } from 'module'; const require = createRequire(import.meta.url); globalThis.__filename = require('url').fileURLToPath(import.meta.url); globalThis.__dirname = require('path').dirname(globalThis.__filename);\" && bash scripts/copy_bundle_assets.sh"
   },
   "bin": {
     "gemini": "bundle/gemini.js"
@@ -34,9 +34,7 @@
     "README.md",
     "LICENSE"
   ],
-  "dependencies": {
-    "sqlite3": "^5.1.7"
-  },
+  "dependencies": {},
   "devDependencies": {
     "@types/mime-types": "^2.1.4",
     "@vitest/coverage-v8": "^3.1.1",