From b3f52e215a98835b752bd3ba3ec08ae44e480eda Mon Sep 17 00:00:00 2001
From: Taylor Mullen <ntaylormullen@google.com>
Date: Mon, 26 May 2025 15:59:19 -0700
Subject: [PATCH] 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-lock.json                       | 1242 +----------------------
 package.json                            |    6 +-
 packages/server/package.json            |    3 +-
 packages/server/src/core/logger.test.ts |  515 +++++++---
 packages/server/src/core/logger.ts      |  298 ++++--
 5 files changed, 589 insertions(+), 1475 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index c0cec25f..8fa88e38 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -10,9 +10,6 @@
       "workspaces": [
         "packages/*"
       ],
-      "dependencies": {
-        "sqlite3": "^5.1.7"
-      },
       "bin": {
         "gemini": "bundle/gemini.js"
       },
@@ -871,13 +868,6 @@
         "node": "^18.18.0 || ^20.9.0 || >=21.1.0"
       }
     },
-    "node_modules/@gar/promisify": {
-      "version": "1.1.3",
-      "resolved": "https://registry.npmjs.org/@gar/promisify/-/promisify-1.1.3.tgz",
-      "integrity": "sha512-k2Ty1JcVojjJFwrg/ThKi2ujJ7XNLYaFGNB/bWT9wGR+oSMJHMa5w+CUq6p/pVrKeNNgA7pCqEcjSnHVoqJQFw==",
-      "license": "MIT",
-      "optional": true
-    },
     "node_modules/@gemini-code/cli": {
       "resolved": "packages/cli",
       "link": true
@@ -1214,45 +1204,6 @@
         "node": ">= 8"
       }
     },
-    "node_modules/@npmcli/fs": {
-      "version": "1.1.1",
-      "resolved": "https://registry.npmjs.org/@npmcli/fs/-/fs-1.1.1.tgz",
-      "integrity": "sha512-8KG5RD0GVP4ydEzRn/I4BNDuxDtqVbOdm8675T49OIG/NGhaK0pjPX7ZcDlvKYbA+ulvVK3ztfcF4uBdOxuJbQ==",
-      "license": "ISC",
-      "optional": true,
-      "dependencies": {
-        "@gar/promisify": "^1.0.1",
-        "semver": "^7.3.5"
-      }
-    },
-    "node_modules/@npmcli/fs/node_modules/semver": {
-      "version": "7.7.2",
-      "resolved": "https://registry.npmjs.org/semver/-/semver-7.7.2.tgz",
-      "integrity": "sha512-RF0Fw+rO5AMf9MAyaRXI4AV0Ulj5lMHqVxxdSgiVbixSCXoEmmX/jk0CuJw4+3SqroYO9VoUh+HcuJivvtJemA==",
-      "license": "ISC",
-      "optional": true,
-      "bin": {
-        "semver": "bin/semver.js"
-      },
-      "engines": {
-        "node": ">=10"
-      }
-    },
-    "node_modules/@npmcli/move-file": {
-      "version": "1.1.2",
-      "resolved": "https://registry.npmjs.org/@npmcli/move-file/-/move-file-1.1.2.tgz",
-      "integrity": "sha512-1SUf/Cg2GzGDyaf15aR9St9TWlb+XvbZXWpDx8YKs7MLzMH/BCeopv+y9vzrzgkfykCGuWOlSu3mZhj2+FQcrg==",
-      "deprecated": "This functionality has been moved to @npmcli/fs",
-      "license": "MIT",
-      "optional": true,
-      "dependencies": {
-        "mkdirp": "^1.0.4",
-        "rimraf": "^3.0.2"
-      },
-      "engines": {
-        "node": ">=10"
-      }
-    },
     "node_modules/@pkgjs/parseargs": {
       "version": "0.11.0",
       "resolved": "https://registry.npmjs.org/@pkgjs/parseargs/-/parseargs-0.11.0.tgz",
@@ -1610,16 +1561,6 @@
         "react-dom": "^18.0.0"
       }
     },
-    "node_modules/@tootallnate/once": {
-      "version": "1.1.2",
-      "resolved": "https://registry.npmjs.org/@tootallnate/once/-/once-1.1.2.tgz",
-      "integrity": "sha512-RbzJvlNzmRq5c3O09UipeuXno4tA1FE6ikOjxZK0tuxVv3412l64l5t1W5pj4+rJq9vpkm/kwiR07aZXnsKPxw==",
-      "license": "MIT",
-      "optional": true,
-      "engines": {
-        "node": ">= 6"
-      }
-    },
     "node_modules/@types/aria-query": {
       "version": "5.0.4",
       "resolved": "https://registry.npmjs.org/@types/aria-query/-/aria-query-5.0.4.tgz",
@@ -2145,13 +2086,6 @@
         "url": "https://opencollective.com/vitest"
       }
     },
-    "node_modules/abbrev": {
-      "version": "1.1.1",
-      "resolved": "https://registry.npmjs.org/abbrev/-/abbrev-1.1.1.tgz",
-      "integrity": "sha512-nne9/IiQ/hzIhY6pdDnbBtz7DjPTKrY00P/zvPSm5pOFkl6xuGrGnXn/VtTNNfNtAfZ9/1RtehkszU9qcTii0Q==",
-      "license": "ISC",
-      "optional": true
-    },
     "node_modules/accepts": {
       "version": "2.0.0",
       "resolved": "https://registry.npmjs.org/accepts/-/accepts-2.0.0.tgz",
@@ -2218,56 +2152,6 @@
         "acorn": "^6.0.0 || ^7.0.0 || ^8.0.0"
       }
     },
-    "node_modules/agent-base": {
-      "version": "6.0.2",
-      "resolved": "https://registry.npmjs.org/agent-base/-/agent-base-6.0.2.tgz",
-      "integrity": "sha512-RZNwNclF7+MS/8bDg70amg32dyeZGZxiDuQmZxKLAlQjr3jGyLx+4Kkk58UO7D2QdgFIQCovuSuZESne6RG6XQ==",
-      "license": "MIT",
-      "optional": true,
-      "dependencies": {
-        "debug": "4"
-      },
-      "engines": {
-        "node": ">= 6.0.0"
-      }
-    },
-    "node_modules/agentkeepalive": {
-      "version": "4.6.0",
-      "resolved": "https://registry.npmjs.org/agentkeepalive/-/agentkeepalive-4.6.0.tgz",
-      "integrity": "sha512-kja8j7PjmncONqaTsB8fQ+wE2mSU2DJ9D4XKoJ5PFWIdRMa6SLSN1ff4mOr4jCbfRSsxR4keIiySJU0N9T5hIQ==",
-      "license": "MIT",
-      "optional": true,
-      "dependencies": {
-        "humanize-ms": "^1.2.1"
-      },
-      "engines": {
-        "node": ">= 8.0.0"
-      }
-    },
-    "node_modules/aggregate-error": {
-      "version": "3.1.0",
-      "resolved": "https://registry.npmjs.org/aggregate-error/-/aggregate-error-3.1.0.tgz",
-      "integrity": "sha512-4I7Td01quW/RpocfNayFdFVk1qSuoh0E7JrbRJ16nH01HhKFQ88INq9Sd+nd72zqRySlr9BmDA8xlEJ6vJMrYA==",
-      "license": "MIT",
-      "optional": true,
-      "dependencies": {
-        "clean-stack": "^2.0.0",
-        "indent-string": "^4.0.0"
-      },
-      "engines": {
-        "node": ">=8"
-      }
-    },
-    "node_modules/aggregate-error/node_modules/indent-string": {
-      "version": "4.0.0",
-      "resolved": "https://registry.npmjs.org/indent-string/-/indent-string-4.0.0.tgz",
-      "integrity": "sha512-EdDDZu4A2OyIK7Lr/2zG+w5jmbuk1DVBnEwREQvBzspBJkCEbRa8GxU1lghYcaGJCnRWibjDXlq779X1/y5xwg==",
-      "license": "MIT",
-      "optional": true,
-      "engines": {
-        "node": ">=8"
-      }
-    },
     "node_modules/ajv": {
       "version": "6.12.6",
       "resolved": "https://registry.npmjs.org/ajv/-/ajv-6.12.6.tgz",
@@ -2323,28 +2207,6 @@
         "url": "https://github.com/chalk/ansi-styles?sponsor=1"
       }
     },
-    "node_modules/aproba": {
-      "version": "2.0.0",
-      "resolved": "https://registry.npmjs.org/aproba/-/aproba-2.0.0.tgz",
-      "integrity": "sha512-lYe4Gx7QT+MKGbDsA+Z+he/Wtef0BiwDOlK/XkBrdfsh9J/jPPXbX0tE9x9cl27Tmu5gg3QUbUrQYa/y+KOHPQ==",
-      "license": "ISC",
-      "optional": true
-    },
-    "node_modules/are-we-there-yet": {
-      "version": "3.0.1",
-      "resolved": "https://registry.npmjs.org/are-we-there-yet/-/are-we-there-yet-3.0.1.tgz",
-      "integrity": "sha512-QZW4EDmGwlYur0Yyf/b2uGucHQMa8aFUP7eu9ddR73vvhFyt4V0Vl3QHPcTNJ8l6qYOBdxgXdnBXQrHilfRQBg==",
-      "deprecated": "This package is no longer supported.",
-      "license": "ISC",
-      "optional": true,
-      "dependencies": {
-        "delegates": "^1.0.0",
-        "readable-stream": "^3.6.0"
-      },
-      "engines": {
-        "node": "^12.13.0 || ^14.15.0 || >=16.0.0"
-      }
-    },
     "node_modules/argparse": {
       "version": "2.0.1",
       "resolved": "https://registry.npmjs.org/argparse/-/argparse-2.0.1.tgz",
@@ -2572,7 +2434,7 @@
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/balanced-match/-/balanced-match-1.0.2.tgz",
       "integrity": "sha512-3oSeUO0TMV67hN1AmbXsK4yaqU7tjiHlbxRDZOpH0KW9+CeX4bRAaX0Anxt0tx2MrpRpWwQaPwIlISEJhYU5Pw==",
-      "devOptional": true,
+      "dev": true,
       "license": "MIT"
     },
     "node_modules/base64-js": {
@@ -2604,26 +2466,6 @@
         "node": "*"
       }
     },
-    "node_modules/bindings": {
-      "version": "1.5.0",
-      "resolved": "https://registry.npmjs.org/bindings/-/bindings-1.5.0.tgz",
-      "integrity": "sha512-p2q/t/mhvuOj/UeLlV6566GD/guowlr0hHxClI0W9m7MWYkL1F0hLo+0Aexs9HSPCtR1SXQ0TD3MMKrXZajbiQ==",
-      "license": "MIT",
-      "dependencies": {
-        "file-uri-to-path": "1.0.0"
-      }
-    },
-    "node_modules/bl": {
-      "version": "4.1.0",
-      "resolved": "https://registry.npmjs.org/bl/-/bl-4.1.0.tgz",
-      "integrity": "sha512-1W07cM9gS6DcLperZfFSj+bWLtaPGSOHWhPiGzXmvVJbRLdG82sH/Kn8EtW1VqWVA54AKf2h5k5BbnIbwF3h6w==",
-      "license": "MIT",
-      "dependencies": {
-        "buffer": "^5.5.0",
-        "inherits": "^2.0.4",
-        "readable-stream": "^3.4.0"
-      }
-    },
     "node_modules/body-parser": {
       "version": "2.2.0",
       "resolved": "https://registry.npmjs.org/body-parser/-/body-parser-2.2.0.tgz",
@@ -2648,7 +2490,7 @@
       "version": "1.1.11",
       "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-1.1.11.tgz",
       "integrity": "sha512-iCuPHDFgrHX7H2vEI/5xpz07zSHB00TpugqhmYtVmMO6518mCuRMoOYFldEBl0g187ufozdaHgWKcYFb61qGiA==",
-      "devOptional": true,
+      "dev": true,
       "license": "MIT",
       "dependencies": {
         "balanced-match": "^1.0.0",
@@ -2667,30 +2509,6 @@
         "node": ">=8"
       }
     },
-    "node_modules/buffer": {
-      "version": "5.7.1",
-      "resolved": "https://registry.npmjs.org/buffer/-/buffer-5.7.1.tgz",
-      "integrity": "sha512-EHcyIPBQ4BSGlvjB16k5KgAJ27CIsHY/2JBmCRReo48y9rQ3MaUzWX3KVlBa4U7MyX02HdVj0K7C3WaB3ju7FQ==",
-      "funding": [
-        {
-          "type": "github",
-          "url": "https://github.com/sponsors/feross"
-        },
-        {
-          "type": "patreon",
-          "url": "https://www.patreon.com/feross"
-        },
-        {
-          "type": "consulting",
-          "url": "https://feross.org/support"
-        }
-      ],
-      "license": "MIT",
-      "dependencies": {
-        "base64-js": "^1.3.1",
-        "ieee754": "^1.1.13"
-      }
-    },
     "node_modules/buffer-equal-constant-time": {
       "version": "1.0.1",
       "resolved": "https://registry.npmjs.org/buffer-equal-constant-time/-/buffer-equal-constant-time-1.0.1.tgz",
@@ -2731,36 +2549,6 @@
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       }
     },
-    "node_modules/cacache": {
-      "version": "15.3.0",
-      "resolved": "https://registry.npmjs.org/cacache/-/cacache-15.3.0.tgz",
-      "integrity": "sha512-VVdYzXEn+cnbXpFgWs5hTT7OScegHVmLhJIR8Ufqk3iFD6A6j5iSX1KuBTfNEv4tdJWE2PzA6IVFtcLC7fN9wQ==",
-      "license": "ISC",
-      "optional": true,
-      "dependencies": {
-        "@npmcli/fs": "^1.0.0",
-        "@npmcli/move-file": "^1.0.1",
-        "chownr": "^2.0.0",
-        "fs-minipass": "^2.0.0",
-        "glob": "^7.1.4",
-        "infer-owner": "^1.0.4",
-        "lru-cache": "^6.0.0",
-        "minipass": "^3.1.1",
-        "minipass-collect": "^1.0.2",
-        "minipass-flush": "^1.0.5",
-        "minipass-pipeline": "^1.2.2",
-        "mkdirp": "^1.0.3",
-        "p-map": "^4.0.0",
-        "promise-inflight": "^1.0.1",
-        "rimraf": "^3.0.2",
-        "ssri": "^8.0.1",
-        "tar": "^6.0.2",
-        "unique-filename": "^1.1.1"
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-      "engines": {
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     "node_modules/call-bind": {
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       "resolved": "https://registry.npmjs.org/call-bind/-/call-bind-1.0.8.tgz",
@@ -2862,25 +2650,6 @@
         "node": ">= 16"
       }
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-    "node_modules/chownr": {
-      "version": "2.0.0",
-      "resolved": "https://registry.npmjs.org/chownr/-/chownr-2.0.0.tgz",
-      "integrity": "sha512-bIomtDF5KGpdogkLd9VspvFzk9KfpyyGlS8YFVZl7TGPBHL5snIOnxeshwVgPteQ9b4Eydl+pVbIyE1DcvCWgQ==",
-      "license": "ISC",
-      "engines": {
-        "node": ">=10"
-      }
-    },
-    "node_modules/clean-stack": {
-      "version": "2.2.0",
-      "resolved": "https://registry.npmjs.org/clean-stack/-/clean-stack-2.2.0.tgz",
-      "integrity": "sha512-4diC9HaTE+KRAMWhDhrGOECgWZxoevMc5TlkObMqNSsVU62PYzXZ/SMTjzyGAFF1YusgxGcSWTEXBhp0CPwQ1A==",
-      "license": "MIT",
-      "optional": true,
-      "engines": {
-        "node": ">=6"
-      }
-    },
     "node_modules/cli-boxes": {
       "version": "3.0.0",
       "resolved": "https://registry.npmjs.org/cli-boxes/-/cli-boxes-3.0.0.tgz",
@@ -3075,30 +2844,13 @@
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     },
-    "node_modules/color-support": {
-      "version": "1.1.3",
-      "resolved": "https://registry.npmjs.org/color-support/-/color-support-1.1.3.tgz",
-      "integrity": "sha512-qiBjkpbMLO/HL68y+lh4q0/O1MZFj2RX6X/KmMa3+gJD3z+WwI1ZzDHysvqHGS3mP6mznPckpXmw1nI9cJjyRg==",
-      "license": "ISC",
-      "optional": true,
-      "bin": {
-        "color-support": "bin.js"
-      }
-    },
     "node_modules/concat-map": {
       "version": "0.0.1",
       "resolved": "https://registry.npmjs.org/concat-map/-/concat-map-0.0.1.tgz",
       "integrity": "sha512-/Srv4dswyQNBfohGpz9o6Yb3Gz3SrUDqBH5rTuhGR7ahtlbYKnVxw2bCFMRljaA7EXHaXZ8wsHdodFvbkhKmqg==",
-      "devOptional": true,
+      "dev": true,
       "license": "MIT"
     },
-    "node_modules/console-control-strings": {
-      "version": "1.1.0",
-      "resolved": "https://registry.npmjs.org/console-control-strings/-/console-control-strings-1.1.0.tgz",
-      "integrity": "sha512-ty/fTekppD2fIwRvnZAVdeOiGd1c7YXEixbgJTNzqcxJWKQnjJ/V1bNEEE6hygpM3WjwHFUVK6HTjWSzV4a8sQ==",
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       "resolved": "https://registry.npmjs.org/content-disposition/-/content-disposition-1.0.0.tgz",
@@ -3287,21 +3039,6 @@
       "dev": true,
       "license": "MIT"
     },
-    "node_modules/decompress-response": {
-      "version": "6.0.0",
-      "resolved": "https://registry.npmjs.org/decompress-response/-/decompress-response-6.0.0.tgz",
-      "integrity": "sha512-aW35yZM6Bb/4oJlZncMH2LCoZtJXTRxES17vE3hoRiowU2kWHaJKFkSBDnDR+cm9J+9QhXmREyIfv0pji9ejCQ==",
-      "license": "MIT",
-      "dependencies": {
-        "mimic-response": "^3.1.0"
-      },
-      "engines": {
-        "node": ">=10"
-      },
-      "funding": {
-        "url": "https://github.com/sponsors/sindresorhus"
-      }
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     "node_modules/deep-eql": {
       "version": "5.0.2",
       "resolved": "https://registry.npmjs.org/deep-eql/-/deep-eql-5.0.2.tgz",
@@ -3345,15 +3082,6 @@
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-    "node_modules/deep-extend": {
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@@ -3437,13 +3165,6 @@
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@@ -3462,15 +3183,6 @@
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-      "resolved": "https://registry.npmjs.org/detect-libc/-/detect-libc-2.0.4.tgz",
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-      "license": "Apache-2.0",
-      "engines": {
-        "node": ">=8"
-      }
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       "version": "1.1.0",
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       "license": "MIT",
       "optional": true,
+      "peer": true,
       "dependencies": {
         "iconv-lite": "^0.6.2"
       }
     },
-    "node_modules/end-of-stream": {
-      "version": "1.4.4",
-      "resolved": "https://registry.npmjs.org/end-of-stream/-/end-of-stream-1.4.4.tgz",
-      "integrity": "sha512-+uw1inIHVPQoaVuHzRyXd21icM+cnt4CzD5rW+NC1wjOUSTOs+Te7FOv7AhN7vS9x/oIyhLP5PR1H+phQAHu5Q==",
-      "license": "MIT",
-      "dependencies": {
-        "once": "^1.4.0"
-      }
-    },
     "node_modules/entities": {
       "version": "6.0.0",
       "resolved": "https://registry.npmjs.org/entities/-/entities-6.0.0.tgz",
@@ -3608,16 +3312,6 @@
         "url": "https://github.com/fb55/entities?sponsor=1"
       }
     },
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@@ -8555,51 +7583,6 @@
       "integrity": "sha512-wnD2ZE+l+SPC/uoS0vXeE9L1+0wuaMqKlfz9AMUo38JsyLSBWSFcHR1Rri62LZc12vLr1gb3jl7iwQhgwpAbGQ==",
       "license": "ISC"
     },
-    "node_modules/simple-concat": {
-      "version": "1.0.1",
-      "resolved": "https://registry.npmjs.org/simple-concat/-/simple-concat-1.0.1.tgz",
-      "integrity": "sha512-cSFtAPtRhljv69IK0hTVZQ+OfE9nePi/rtJmw5UjHeVyVroEqJXP1sFztKUy1qU+xvz3u/sfYJLa947b7nAN2Q==",
-      "funding": [
-        {
-          "type": "github",
-          "url": "https://github.com/sponsors/feross"
-        },
-        {
-          "type": "patreon",
-          "url": "https://www.patreon.com/feross"
-        },
-        {
-          "type": "consulting",
-          "url": "https://feross.org/support"
-        }
-      ],
-      "license": "MIT"
-    },
-    "node_modules/simple-get": {
-      "version": "4.0.1",
-      "resolved": "https://registry.npmjs.org/simple-get/-/simple-get-4.0.1.tgz",
-      "integrity": "sha512-brv7p5WgH0jmQJr1ZDDfKDOSeWWg+OVypG99A/5vYGPqJ6pxiaHLy8nxtFjBA7oMa01ebA9gfh1uMCFqOuXxvA==",
-      "funding": [
-        {
-          "type": "github",
-          "url": "https://github.com/sponsors/feross"
-        },
-        {
-          "type": "patreon",
-          "url": "https://www.patreon.com/feross"
-        },
-        {
-          "type": "consulting",
-          "url": "https://feross.org/support"
-        }
-      ],
-      "license": "MIT",
-      "dependencies": {
-        "decompress-response": "^6.0.0",
-        "once": "^1.3.1",
-        "simple-concat": "^1.0.0"
-      }
-    },
     "node_modules/slice-ansi": {
       "version": "7.1.0",
       "resolved": "https://registry.npmjs.org/slice-ansi/-/slice-ansi-7.1.0.tgz",
@@ -8643,47 +7626,6 @@
         "url": "https://github.com/sponsors/sindresorhus"
       }
     },
-    "node_modules/smart-buffer": {
-      "version": "4.2.0",
-      "resolved": "https://registry.npmjs.org/smart-buffer/-/smart-buffer-4.2.0.tgz",
-      "integrity": "sha512-94hK0Hh8rPqQl2xXc3HsaBoOXKV20MToPkcXvwbISWLEs+64sBq5kFgn2kJDHb1Pry9yrP0dxrCI9RRci7RXKg==",
-      "license": "MIT",
-      "optional": true,
-      "engines": {
-        "node": ">= 6.0.0",
-        "npm": ">= 3.0.0"
-      }
-    },
-    "node_modules/socks": {
-      "version": "2.8.4",
-      "resolved": "https://registry.npmjs.org/socks/-/socks-2.8.4.tgz",
-      "integrity": "sha512-D3YaD0aRxR3mEcqnidIs7ReYJFVzWdd6fXJYUM8ixcQcJRGTka/b3saV0KflYhyVJXKhb947GndU35SxYNResQ==",
-      "license": "MIT",
-      "optional": true,
-      "dependencies": {
-        "ip-address": "^9.0.5",
-        "smart-buffer": "^4.2.0"
-      },
-      "engines": {
-        "node": ">= 10.0.0",
-        "npm": ">= 3.0.0"
-      }
-    },
-    "node_modules/socks-proxy-agent": {
-      "version": "6.2.1",
-      "resolved": "https://registry.npmjs.org/socks-proxy-agent/-/socks-proxy-agent-6.2.1.tgz",
-      "integrity": "sha512-a6KW9G+6B3nWZ1yB8G7pJwL3ggLy1uTzKAgCb7ttblwqdz9fMGJUuTy3uFzEP48FAs9FLILlmzDlE2JJhVQaXQ==",
-      "license": "MIT",
-      "optional": true,
-      "dependencies": {
-        "agent-base": "^6.0.2",
-        "debug": "^4.3.3",
-        "socks": "^2.6.2"
-      },
-      "engines": {
-        "node": ">= 10"
-      }
-    },
     "node_modules/source-map-js": {
       "version": "1.2.1",
       "resolved": "https://registry.npmjs.org/source-map-js/-/source-map-js-1.2.1.tgz",
@@ -8726,50 +7668,6 @@
       "integrity": "sha512-Bvg/8F5XephndSK3JffaRqdT+gyhfqIPwDHpX80tJrF8QQRYMo8sNMeaZ2Dp5+jhwKnUmIOyFFQfHRkjJm5nXg==",
       "license": "CC0-1.0"
     },
-    "node_modules/sprintf-js": {
-      "version": "1.1.3",
-      "resolved": "https://registry.npmjs.org/sprintf-js/-/sprintf-js-1.1.3.tgz",
-      "integrity": "sha512-Oo+0REFV59/rz3gfJNKQiBlwfHaSESl1pcGyABQsnnIfWOFt6JNj5gCog2U6MLZ//IGYD+nA8nI+mTShREReaA==",
-      "license": "BSD-3-Clause",
-      "optional": true
-    },
-    "node_modules/sqlite3": {
-      "version": "5.1.7",
-      "resolved": "https://registry.npmjs.org/sqlite3/-/sqlite3-5.1.7.tgz",
-      "integrity": "sha512-GGIyOiFaG+TUra3JIfkI/zGP8yZYLPQ0pl1bH+ODjiX57sPhrLU5sQJn1y9bDKZUFYkX1crlrPfSYt0BKKdkog==",
-      "hasInstallScript": true,
-      "license": "BSD-3-Clause",
-      "dependencies": {
-        "bindings": "^1.5.0",
-        "node-addon-api": "^7.0.0",
-        "prebuild-install": "^7.1.1",
-        "tar": "^6.1.11"
-      },
-      "optionalDependencies": {
-        "node-gyp": "8.x"
-      },
-      "peerDependencies": {
-        "node-gyp": "8.x"
-      },
-      "peerDependenciesMeta": {
-        "node-gyp": {
-          "optional": true
-        }
-      }
-    },
-    "node_modules/ssri": {
-      "version": "8.0.1",
-      "resolved": "https://registry.npmjs.org/ssri/-/ssri-8.0.1.tgz",
-      "integrity": "sha512-97qShzy1AiyxvPNIkLWoGua7xoQzzPjQ0HAH4B0rWKo7SZ6USuPcrUiAFrws0UH8RrbWmgq3LMTObhPIHbbBeQ==",
-      "license": "ISC",
-      "optional": true,
-      "dependencies": {
-        "minipass": "^3.1.1"
-      },
-      "engines": {
-        "node": ">= 8"
-      }
-    },
     "node_modules/stack-utils": {
       "version": "2.0.6",
       "resolved": "https://registry.npmjs.org/stack-utils/-/stack-utils-2.0.6.tgz",
@@ -8828,15 +7726,6 @@
         "node": ">= 0.4"
       }
     },
-    "node_modules/string_decoder": {
-      "version": "1.3.0",
-      "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.3.0.tgz",
-      "integrity": "sha512-hkRX8U1WjJFd8LsDJ2yQ/wWWxaopEsABU1XfkM8A+j0+85JAGppt16cr1Whg6KIbb4okU6Mql6BOj+uup/wKeA==",
-      "license": "MIT",
-      "dependencies": {
-        "safe-buffer": "~5.2.0"
-      }
-    },
     "node_modules/string-width": {
       "version": "4.2.3",
       "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.3.tgz",
@@ -9064,66 +7953,6 @@
       "dev": true,
       "license": "MIT"
     },
-    "node_modules/tar": {
-      "version": "6.2.1",
-      "resolved": "https://registry.npmjs.org/tar/-/tar-6.2.1.tgz",
-      "integrity": "sha512-DZ4yORTwrbTj/7MZYq2w+/ZFdI6OZ/f9SFHR+71gIVUZhOQPHzVCLpvRnPgyaMpfWxxk/4ONva3GQSyNIKRv6A==",
-      "license": "ISC",
-      "dependencies": {
-        "chownr": "^2.0.0",
-        "fs-minipass": "^2.0.0",
-        "minipass": "^5.0.0",
-        "minizlib": "^2.1.1",
-        "mkdirp": "^1.0.3",
-        "yallist": "^4.0.0"
-      },
-      "engines": {
-        "node": ">=10"
-      }
-    },
-    "node_modules/tar-fs": {
-      "version": "2.1.3",
-      "resolved": "https://registry.npmjs.org/tar-fs/-/tar-fs-2.1.3.tgz",
-      "integrity": "sha512-090nwYJDmlhwFwEW3QQl+vaNnxsO2yVsd45eTKRBzSzu+hlb1w2K9inVq5b0ngXuLVqQ4ApvsUHHnu/zQNkWAg==",
-      "license": "MIT",
-      "dependencies": {
-        "chownr": "^1.1.1",
-        "mkdirp-classic": "^0.5.2",
-        "pump": "^3.0.0",
-        "tar-stream": "^2.1.4"
-      }
-    },
-    "node_modules/tar-fs/node_modules/chownr": {
-      "version": "1.1.4",
-      "resolved": "https://registry.npmjs.org/chownr/-/chownr-1.1.4.tgz",
-      "integrity": "sha512-jJ0bqzaylmJtVnNgzTeSOs8DPavpbYgEr/b0YL8/2GO3xJEhInFmhKMUnEJQjZumK7KXGFhUy89PrsJWlakBVg==",
-      "license": "ISC"
-    },
-    "node_modules/tar-stream": {
-      "version": "2.2.0",
-      "resolved": "https://registry.npmjs.org/tar-stream/-/tar-stream-2.2.0.tgz",
-      "integrity": "sha512-ujeqbceABgwMZxEJnk2HDY2DlnUZ+9oEcb1KzTVfYHio0UE6dG71n60d8D2I4qNvleWrrXpmjpt7vZeF1LnMZQ==",
-      "license": "MIT",
-      "dependencies": {
-        "bl": "^4.0.3",
-        "end-of-stream": "^1.4.1",
-        "fs-constants": "^1.0.0",
-        "inherits": "^2.0.3",
-        "readable-stream": "^3.1.1"
-      },
-      "engines": {
-        "node": ">=6"
-      }
-    },
-    "node_modules/tar/node_modules/minipass": {
-      "version": "5.0.0",
-      "resolved": "https://registry.npmjs.org/minipass/-/minipass-5.0.0.tgz",
-      "integrity": "sha512-3FnjYuehv9k6ovOEbyOswadCDPX1piCfhV8ncmYtHOjuPwylVWsghTLo7rabjC3Rx5xD4HDx8Wm1xnMF7S5qFQ==",
-      "license": "ISC",
-      "engines": {
-        "node": ">=8"
-      }
-    },
     "node_modules/test-exclude": {
       "version": "7.0.1",
       "resolved": "https://registry.npmjs.org/test-exclude/-/test-exclude-7.0.1.tgz",
@@ -9406,18 +8235,6 @@
         "strip-bom": "^3.0.0"
       }
     },
-    "node_modules/tunnel-agent": {
-      "version": "0.6.0",
-      "resolved": "https://registry.npmjs.org/tunnel-agent/-/tunnel-agent-0.6.0.tgz",
-      "integrity": "sha512-McnNiV1l8RYeY8tBgEpuodCC1mLUdbSN+CYBL7kJsJNInOP8UjDDEwdk6Mw60vdLLrr5NHKZhMAOSrR2NZuQ+w==",
-      "license": "Apache-2.0",
-      "dependencies": {
-        "safe-buffer": "^5.0.1"
-      },
-      "engines": {
-        "node": "*"
-      }
-    },
     "node_modules/type-check": {
       "version": "0.4.0",
       "resolved": "https://registry.npmjs.org/type-check/-/type-check-0.4.0.tgz",
@@ -9631,26 +8448,6 @@
         "url": "https://github.com/sponsors/sindresorhus"
       }
     },
-    "node_modules/unique-filename": {
-      "version": "1.1.1",
-      "resolved": "https://registry.npmjs.org/unique-filename/-/unique-filename-1.1.1.tgz",
-      "integrity": "sha512-Vmp0jIp2ln35UTXuryvjzkjGdRyf9b2lTXuSYUiPmzRcl3FDtYqAwOnTJkAngD9SWhnoJzDbTKwaOrZ+STtxNQ==",
-      "license": "ISC",
-      "optional": true,
-      "dependencies": {
-        "unique-slug": "^2.0.0"
-      }
-    },
-    "node_modules/unique-slug": {
-      "version": "2.0.2",
-      "resolved": "https://registry.npmjs.org/unique-slug/-/unique-slug-2.0.2.tgz",
-      "integrity": "sha512-zoWr9ObaxALD3DOPfjPSqxt4fnZiWblxHIgeWqW8x7UqDzEtHEQLzji2cuJYQFCU6KmoJikOYAZlrTHHebjx2w==",
-      "license": "ISC",
-      "optional": true,
-      "dependencies": {
-        "imurmurhash": "^0.1.4"
-      }
-    },
     "node_modules/unpipe": {
       "version": "1.0.0",
       "resolved": "https://registry.npmjs.org/unpipe/-/unpipe-1.0.0.tgz",
@@ -9669,12 +8466,6 @@
         "punycode": "^2.1.0"
       }
     },
-    "node_modules/util-deprecate": {
-      "version": "1.0.2",
-      "resolved": "https://registry.npmjs.org/util-deprecate/-/util-deprecate-1.0.2.tgz",
-      "integrity": "sha512-EPD5q1uXyFxJpCrLnCc1nHnq3gOa6DZBocAIiI2TaSCA7VCJ1UJDMagCzIkXNsUYfD1daK//LTEQ8xiIbrHtcw==",
-      "license": "MIT"
-    },
     "node_modules/uuid": {
       "version": "9.0.1",
       "resolved": "https://registry.npmjs.org/uuid/-/uuid-9.0.1.tgz",
@@ -10085,16 +8876,6 @@
         "node": ">=8"
       }
     },
-    "node_modules/wide-align": {
-      "version": "1.1.5",
-      "resolved": "https://registry.npmjs.org/wide-align/-/wide-align-1.1.5.tgz",
-      "integrity": "sha512-eDMORYaPNZ4sQIuuYPDHdQvf4gyCF9rEEV/yPxGfwPkRodwEgiMUUXTx/dex+Me0wxx53S+NgUHaP7y3MGlDmg==",
-      "license": "ISC",
-      "optional": true,
-      "dependencies": {
-        "string-width": "^1.0.2 || 2 || 3 || 4"
-      }
-    },
     "node_modules/widest-line": {
       "version": "5.0.0",
       "resolved": "https://registry.npmjs.org/widest-line/-/widest-line-5.0.0.tgz",
@@ -10322,12 +9103,6 @@
         "node": ">=10"
       }
     },
-    "node_modules/yallist": {
-      "version": "4.0.0",
-      "resolved": "https://registry.npmjs.org/yallist/-/yallist-4.0.0.tgz",
-      "integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==",
-      "license": "ISC"
-    },
     "node_modules/yargs": {
       "version": "17.7.2",
       "resolved": "https://registry.npmjs.org/yargs/-/yargs-17.7.2.tgz",
@@ -10495,8 +9270,7 @@
         "diff": "^7.0.0",
         "dotenv": "^16.4.7",
         "fast-glob": "^3.3.3",
-        "shell-quote": "^1.8.2",
-        "sqlite3": "^5.1.7"
+        "shell-quote": "^1.8.2"
       },
       "devDependencies": {
         "@types/diff": "^7.0.2",
diff --git a/package.json b/package.json
index 61366e41..82d18391 100644
--- a/package.json
+++ b/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",
diff --git a/packages/server/package.json b/packages/server/package.json
index a9bb8f94..8e654c88 100644
--- a/packages/server/package.json
+++ b/packages/server/package.json
@@ -27,8 +27,7 @@
     "diff": "^7.0.0",
     "dotenv": "^16.4.7",
     "fast-glob": "^3.3.3",
-    "shell-quote": "^1.8.2",
-    "sqlite3": "^5.1.7"
+    "shell-quote": "^1.8.2"
   },
   "devDependencies": {
     "@types/diff": "^7.0.2",
diff --git a/packages/server/src/core/logger.test.ts b/packages/server/src/core/logger.test.ts
index 9b4f4555..2663a6be 100644
--- a/packages/server/src/core/logger.test.ts
+++ b/packages/server/src/core/logger.test.ts
@@ -4,194 +4,429 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest';
-import { Logger, MessageSenderType } from './logger.js';
+import {
+  describe,
+  it,
+  expect,
+  vi,
+  beforeEach,
+  afterEach,
+  afterAll,
+} from 'vitest';
+import { Logger, MessageSenderType, LogEntry } from './logger.js';
+import { promises as fs } from 'node:fs';
+import path from 'node:path';
 
-// Mocks
-const mockDb = {
-  exec: vi.fn((_sql, callback) => callback?.(null)),
-  all: vi.fn((_sql, _params, callback) => callback?.(null, [])),
-  run: vi.fn((_sql, _params, callback) => callback?.(null)),
-  close: vi.fn((callback) => callback?.(null)),
-};
+const GEMINI_DIR = '.gemini';
+const LOG_FILE_NAME = 'logs.json';
+const TEST_LOG_FILE_PATH = path.join(process.cwd(), GEMINI_DIR, LOG_FILE_NAME);
 
-vi.mock('sqlite3', () => ({
-  Database: vi.fn((_dbPath, _options, callback) => {
-    process.nextTick(() => callback?.(null));
-    return mockDb;
-  }),
-  default: {
-    Database: vi.fn((_dbPath, _options, callback) => {
-      process.nextTick(() => callback?.(null));
-      return mockDb;
-    }),
-  },
-}));
+async function cleanupLogFile() {
+  try {
+    await fs.unlink(TEST_LOG_FILE_PATH);
+  } catch (error) {
+    if ((error as NodeJS.ErrnoException).code !== 'ENOENT') {
+      // Other errors during unlink are ignored for cleanup purposes
+    }
+  }
+  try {
+    const geminiDirPath = path.join(process.cwd(), GEMINI_DIR);
+    const dirContents = await fs.readdir(geminiDirPath);
+    for (const file of dirContents) {
+      if (file.startsWith(LOG_FILE_NAME + '.') && file.endsWith('.bak')) {
+        try {
+          await fs.unlink(path.join(geminiDirPath, file));
+        } catch (_e) {
+          /* ignore */
+        }
+      }
+    }
+  } catch (error) {
+    if ((error as NodeJS.ErrnoException).code !== 'ENOENT') {
+      /* ignore if .gemini dir itself is missing */
+    }
+  }
+}
+
+async function readLogFile(): Promise<LogEntry[]> {
+  try {
+    const content = await fs.readFile(TEST_LOG_FILE_PATH, 'utf-8');
+    return JSON.parse(content) as LogEntry[];
+  } catch (error) {
+    if ((error as NodeJS.ErrnoException).code === 'ENOENT') {
+      return [];
+    }
+    throw error;
+  }
+}
 
 describe('Logger', () => {
   let logger: Logger;
 
   beforeEach(async () => {
-    vi.resetAllMocks();
-
-    // Get a new instance for each test to ensure isolation,
+    vi.useFakeTimers();
+    vi.setSystemTime(new Date('2025-01-01T12:00:00.000Z'));
+    await cleanupLogFile();
     logger = new Logger();
-    // We need to wait for the async initialize to complete
-    await logger.initialize().catch((err) => {
-      console.error('Error initializing logger:', err);
-    });
+    // Initialize is usually called here, but some tests initialize their own instances.
+    // For tests that use the global `logger`, it will be initialized here.
+    await logger.initialize();
   });
 
-  afterEach(() => {
-    vi.restoreAllMocks();
-    logger.close(); // Close the database connection after each test
+  afterEach(async () => {
+    logger.close();
+    await cleanupLogFile();
+    vi.useRealTimers();
+    vi.resetAllMocks(); // Ensure mocks are reset for every test
+  });
+
+  afterAll(async () => {
+    await cleanupLogFile();
   });
 
   describe('initialize', () => {
-    it('should execute create tables if not exists', async () => {
-      expect(mockDb.exec).toHaveBeenCalledWith(
-        expect.stringMatching(/CREATE TABLE IF NOT EXISTS messages/),
-        expect.any(Function),
-      );
+    it('should create .gemini directory and an empty log file if none exist', async () => {
+      await cleanupLogFile();
+      const geminiDirPath = path.join(process.cwd(), GEMINI_DIR);
+      try {
+        await fs.rm(geminiDirPath, { recursive: true, force: true });
+      } catch (_e) {
+        /* ignore */
+      }
+
+      const newLogger = new Logger();
+      await newLogger.initialize();
+
+      const dirExists = await fs
+        .access(geminiDirPath)
+        .then(() => true)
+        .catch(() => false);
+      expect(dirExists).toBe(true);
+      const fileExists = await fs
+        .access(TEST_LOG_FILE_PATH)
+        .then(() => true)
+        .catch(() => false);
+      expect(fileExists).toBe(true);
+      const logContent = await readLogFile();
+      expect(logContent).toEqual([]);
+      newLogger.close();
+    });
+
+    it('should load existing logs and set correct messageId for the current session', async () => {
+      const fixedTime = new Date('2025-01-01T10:00:00.000Z');
+      vi.setSystemTime(fixedTime);
+      const currentSessionId = Math.floor(fixedTime.getTime() / 1000);
+      const existingLogs: LogEntry[] = [
+        {
+          sessionId: currentSessionId,
+          messageId: 0,
+          timestamp: new Date('2025-01-01T10:00:05.000Z').toISOString(),
+          type: MessageSenderType.USER,
+          message: 'Msg1',
+        },
+        {
+          sessionId: currentSessionId - 100,
+          messageId: 5,
+          timestamp: new Date('2025-01-01T09:00:00.000Z').toISOString(),
+          type: MessageSenderType.USER,
+          message: 'OldMsg',
+        },
+        {
+          sessionId: currentSessionId,
+          messageId: 1,
+          timestamp: new Date('2025-01-01T10:00:10.000Z').toISOString(),
+          type: MessageSenderType.USER,
+          message: 'Msg2',
+        },
+      ];
+      await fs.mkdir(path.join(process.cwd(), GEMINI_DIR), { recursive: true });
+      await fs.writeFile(TEST_LOG_FILE_PATH, JSON.stringify(existingLogs));
+      const newLogger = new Logger();
+      await newLogger.initialize();
+      expect(newLogger['messageId']).toBe(2);
+      expect(newLogger['logs']).toEqual(existingLogs);
+      newLogger.close();
+    });
+
+    it('should set messageId to 0 for a new session if log file exists but has no logs for current session', async () => {
+      const fixedTime = new Date('2025-01-01T14:00:00.000Z');
+      vi.setSystemTime(fixedTime);
+      const existingLogs: LogEntry[] = [
+        {
+          sessionId: Math.floor(fixedTime.getTime() / 1000) - 500,
+          messageId: 5,
+          timestamp: new Date().toISOString(),
+          type: MessageSenderType.USER,
+          message: 'OldMsg',
+        },
+      ];
+      await fs.mkdir(path.join(process.cwd(), GEMINI_DIR), { recursive: true });
+      await fs.writeFile(TEST_LOG_FILE_PATH, JSON.stringify(existingLogs));
+      const newLogger = new Logger();
+      await newLogger.initialize();
+      expect(newLogger['messageId']).toBe(0);
+      newLogger.close();
     });
 
     it('should be idempotent', async () => {
-      mockDb.exec.mockClear();
+      // logger is initialized in beforeEach
+      await logger.logMessage(MessageSenderType.USER, 'test message');
+      const initialMessageId = logger['messageId'];
+      const initialLogCount = logger['logs'].length;
+      await logger.initialize(); // Second call should not change state
+      expect(logger['messageId']).toBe(initialMessageId);
+      expect(logger['logs'].length).toBe(initialLogCount);
+      const logsFromFile = await readLogFile();
+      expect(logsFromFile.length).toBe(1);
+    });
 
-      await logger.initialize(); // Second call
+    it('should handle invalid JSON in log file by backing it up and starting fresh', async () => {
+      await fs.mkdir(path.join(process.cwd(), GEMINI_DIR), { recursive: true });
+      await fs.writeFile(TEST_LOG_FILE_PATH, 'invalid json');
+      const consoleDebugSpy = vi
+        .spyOn(console, 'debug')
+        .mockImplementation(() => {});
+      const newLogger = new Logger();
+      await newLogger.initialize();
+      expect(consoleDebugSpy).toHaveBeenCalledWith(
+        expect.stringContaining('Invalid JSON in log file'),
+        expect.any(SyntaxError),
+      );
+      const logContent = await readLogFile();
+      expect(logContent).toEqual([]);
+      const dirContents = await fs.readdir(
+        path.join(process.cwd(), GEMINI_DIR),
+      );
+      expect(
+        dirContents.some(
+          (f) =>
+            f.startsWith(LOG_FILE_NAME + '.invalid_json') && f.endsWith('.bak'),
+        ),
+      ).toBe(true);
+      consoleDebugSpy.mockRestore();
+      newLogger.close();
+    });
 
-      expect(mockDb.exec).not.toHaveBeenCalled();
+    it('should handle non-array JSON in log file by backing it up and starting fresh', async () => {
+      await fs.mkdir(path.join(process.cwd(), GEMINI_DIR), { recursive: true });
+      await fs.writeFile(
+        TEST_LOG_FILE_PATH,
+        JSON.stringify({ not: 'an array' }),
+      );
+      const consoleDebugSpy = vi
+        .spyOn(console, 'debug')
+        .mockImplementation(() => {});
+      const newLogger = new Logger();
+      await newLogger.initialize();
+      expect(consoleDebugSpy).toHaveBeenCalledWith(
+        `Log file at ${TEST_LOG_FILE_PATH} is not a valid JSON array. Starting with empty logs.`,
+      );
+      const logContent = await readLogFile();
+      expect(logContent).toEqual([]);
+      const dirContents = await fs.readdir(
+        path.join(process.cwd(), GEMINI_DIR),
+      );
+      expect(
+        dirContents.some(
+          (f) =>
+            f.startsWith(LOG_FILE_NAME + '.malformed_array') &&
+            f.endsWith('.bak'),
+        ),
+      ).toBe(true);
+      consoleDebugSpy.mockRestore();
+      newLogger.close();
     });
   });
 
   describe('logMessage', () => {
-    it('should insert a message into the database', async () => {
-      const type = MessageSenderType.USER;
-      const message = 'Hello, world!';
-      await logger.logMessage(type, message);
-      expect(mockDb.run).toHaveBeenCalledWith(
-        "INSERT INTO messages (session_id, message_id, type, message, timestamp) VALUES (?, ?, ?, ?, datetime('now'))",
-        [expect.any(Number), 0, type, message], // sessionId, messageId, type, message
-        expect.any(Function),
-      );
+    it('should append a message to the log file and update in-memory logs', async () => {
+      await logger.logMessage(MessageSenderType.USER, 'Hello, world!');
+      const logsFromFile = await readLogFile();
+      expect(logsFromFile.length).toBe(1);
+      expect(logsFromFile[0]).toMatchObject({
+        sessionId: logger['sessionId'],
+        messageId: 0,
+        type: MessageSenderType.USER,
+        message: 'Hello, world!',
+        timestamp: new Date('2025-01-01T12:00:00.000Z').toISOString(),
+      });
+      expect(logger['logs'].length).toBe(1);
+      expect(logger['logs'][0]).toEqual(logsFromFile[0]);
+      expect(logger['messageId']).toBe(1);
     });
 
-    it('should increment messageId for subsequent messages', async () => {
-      await logger.logMessage(MessageSenderType.USER, 'First message');
-      expect(mockDb.run).toHaveBeenCalledWith(
-        expect.any(String),
-        [expect.any(Number), 0, MessageSenderType.USER, 'First message'],
-        expect.any(Function),
-      );
-      await logger.logMessage(MessageSenderType.USER, 'Second message');
-      expect(mockDb.run).toHaveBeenCalledWith(
-        expect.any(String),
-        [expect.any(Number), 1, MessageSenderType.USER, 'Second message'], // messageId is now 1
-        expect.any(Function),
-      );
+    it('should correctly increment messageId for subsequent messages in the same session', async () => {
+      await logger.logMessage(MessageSenderType.USER, 'First');
+      vi.advanceTimersByTime(1000);
+      await logger.logMessage(MessageSenderType.USER, 'Second');
+      const logs = await readLogFile();
+      expect(logs.length).toBe(2);
+      expect(logs[0].messageId).toBe(0);
+      expect(logs[1].messageId).toBe(1);
+      expect(logs[1].timestamp).not.toBe(logs[0].timestamp);
+      expect(logger['messageId']).toBe(2);
     });
 
-    it('should handle database not initialized', async () => {
+    it('should handle logger not initialized', async () => {
       const uninitializedLogger = new Logger();
-      // uninitializedLogger.initialize() is not called
-      const consoleErrorSpy = vi
-        .spyOn(console, 'error')
+      const consoleDebugSpy = vi
+        .spyOn(console, 'debug')
         .mockImplementation(() => {});
-
       await uninitializedLogger.logMessage(MessageSenderType.USER, 'test');
-
-      expect(consoleErrorSpy).toHaveBeenCalledWith('Database not initialized.');
-      expect(mockDb.run).not.toHaveBeenCalled();
-      consoleErrorSpy.mockRestore();
+      expect(consoleDebugSpy).toHaveBeenCalledWith(
+        'Logger not initialized or session ID missing. Cannot log message.',
+      );
+      expect((await readLogFile()).length).toBe(0);
+      consoleDebugSpy.mockRestore();
+      uninitializedLogger.close();
     });
 
-    it('should handle error during db.run', async () => {
-      const error = new Error('db.run failed');
-      mockDb.run.mockImplementationOnce(
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        (_sql: any, _params: any, callback: any) => callback?.(error),
-      );
+    it('should simulate concurrent writes from different logger instances to the same file', async () => {
+      const logger1 = new Logger(); // logger1
+      vi.setSystemTime(new Date('2025-01-01T13:00:00.000Z'));
+      await logger1.initialize();
+      const s1 = logger1['sessionId'];
 
-      await expect(
-        logger.logMessage(MessageSenderType.USER, 'test'),
-      ).rejects.toThrow('db.run failed');
+      const logger2 = new Logger(); // logger2, will share same session if time is same
+      vi.setSystemTime(new Date('2025-01-01T13:00:00.000Z'));
+      await logger2.initialize();
+      expect(logger2['sessionId']).toEqual(s1);
+
+      // Log from logger1
+      await logger1.logMessage(MessageSenderType.USER, 'L1M1'); // L1 internal msgId becomes 1, writes {s1, 0}
+      vi.advanceTimersByTime(10);
+
+      // Log from logger2. It reads file (sees {s1,0}), its internal msgId for s1 is 1.
+      await logger2.logMessage(MessageSenderType.USER, 'L2M1'); // L2 internal msgId becomes 2, writes {s1, 1}
+      vi.advanceTimersByTime(10);
+
+      // Log from logger1. It reads file (sees {s1,0}, {s1,1}), its internal msgId for s1 is 2.
+      await logger1.logMessage(MessageSenderType.USER, 'L1M2'); // L1 internal msgId becomes 3, writes {s1, 2}
+      vi.advanceTimersByTime(10);
+
+      // Log from logger2. It reads file (sees {s1,0}, {s1,1}, {s1,2}), its internal msgId for s1 is 3.
+      await logger2.logMessage(MessageSenderType.USER, 'L2M2'); // L2 internal msgId becomes 4, writes {s1, 3}
+
+      const logsFromFile = await readLogFile();
+      expect(logsFromFile.length).toBe(4);
+      const messageIdsInFile = logsFromFile
+        .map((log) => log.messageId)
+        .sort((a, b) => a - b);
+      expect(messageIdsInFile).toEqual([0, 1, 2, 3]);
+
+      const messagesInFile = logsFromFile
+        .sort((a, b) => a.messageId - b.messageId)
+        .map((l) => l.message);
+      expect(messagesInFile).toEqual(['L1M1', 'L2M1', 'L1M2', 'L2M2']);
+
+      // Check internal state (next messageId each logger would use for that session)
+      expect(logger1['messageId']).toBe(3); // L1 wrote 0, then 2. Next is 3.
+      expect(logger2['messageId']).toBe(4); // L2 wrote 1, then 3. Next is 4.
+
+      logger1.close();
+      logger2.close();
+    });
+
+    it('should not throw, not increment messageId, and log error if writing to file fails', async () => {
+      const writeFileSpy = vi
+        .spyOn(fs, 'writeFile')
+        .mockRejectedValueOnce(new Error('Disk full'));
+      const consoleDebugSpy = vi
+        .spyOn(console, 'debug')
+        .mockImplementation(() => {});
+      const initialMessageId = logger['messageId'];
+      const initialLogCount = logger['logs'].length;
+
+      await logger.logMessage(MessageSenderType.USER, 'test fail write');
+
+      expect(consoleDebugSpy).toHaveBeenCalledWith(
+        'Error writing to log file:',
+        expect.any(Error),
+      );
+      expect(logger['messageId']).toBe(initialMessageId); // Not incremented
+      expect(logger['logs'].length).toBe(initialLogCount); // Log not added to in-memory cache
+
+      writeFileSpy.mockRestore();
+      consoleDebugSpy.mockRestore();
     });
   });
 
   describe('getPreviousUserMessages', () => {
-    it('should query the database for messages', async () => {
-      mockDb.all.mockImplementationOnce(
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        (_sql: any, params: any, callback: any) =>
-          callback?.(null, [{ message: 'msg1' }, { message: 'msg2' }]),
-      );
+    it('should retrieve user messages, sorted newest first by session, then timestamp, then messageId', async () => {
+      const loggerSort = new Logger();
+      vi.setSystemTime(new Date('2025-01-01T10:00:00.000Z'));
+      await loggerSort.initialize();
+      const s1 = loggerSort['sessionId']!;
+      await loggerSort.logMessage(MessageSenderType.USER, 'S1M0_ts100000'); // msgId 0
+      vi.advanceTimersByTime(10);
+      await loggerSort.logMessage(MessageSenderType.USER, 'S1M1_ts100010'); // msgId 1
+      loggerSort.close(); // Close to ensure next initialize starts a new session if time changed
 
+      vi.setSystemTime(new Date('2025-01-01T11:00:00.000Z'));
+      await loggerSort.initialize(); // Re-initialize for a new session
+      const s2 = loggerSort['sessionId']!;
+      expect(s2).not.toEqual(s1);
+      await loggerSort.logMessage(MessageSenderType.USER, 'S2M0_ts110000'); // msgId 0 for s2
+      vi.advanceTimersByTime(10);
+      await loggerSort.logMessage(
+        'model' as MessageSenderType,
+        'S2_Model_ts110010',
+      );
+      vi.advanceTimersByTime(10);
+      await loggerSort.logMessage(MessageSenderType.USER, 'S2M1_ts110020'); // msgId 1 for s2
+      loggerSort.close();
+
+      // To test the sorting thoroughly, especially the session part, we'll read the file
+      // as if it was written by multiple sessions and then initialize a new logger to load them.
+      const combinedLogs = await readLogFile();
+      const finalLogger = new Logger();
+      // Manually set its internal logs to simulate loading from a file with mixed sessions
+      finalLogger['logs'] = combinedLogs;
+      finalLogger['initialized'] = true; // Mark as initialized to allow getPreviousUserMessages to run
+
+      const messages = await finalLogger.getPreviousUserMessages();
+      expect(messages).toEqual([
+        'S2M1_ts110020',
+        'S2M0_ts110000',
+        'S1M1_ts100010',
+        'S1M0_ts100000',
+      ]);
+      finalLogger.close();
+    });
+
+    it('should return empty array if no user messages exist', async () => {
+      await logger.logMessage('system' as MessageSenderType, 'System boot');
       const messages = await logger.getPreviousUserMessages();
-
-      expect(mockDb.all).toHaveBeenCalledWith(
-        expect.stringMatching(/SELECT message FROM messages/),
-        [],
-        expect.any(Function),
-      );
-      expect(messages).toEqual(['msg1', 'msg2']);
-    });
-
-    it('should handle database not initialized', async () => {
-      const uninitializedLogger = new Logger();
-      // uninitializedLogger.initialize() is not called
-      const consoleErrorSpy = vi
-        .spyOn(console, 'error')
-        .mockImplementation(() => {});
-
-      const messages = await uninitializedLogger.getPreviousUserMessages();
-
-      expect(consoleErrorSpy).toHaveBeenCalledWith('Database not initialized.');
       expect(messages).toEqual([]);
-      expect(mockDb.all).not.toHaveBeenCalled();
-      consoleErrorSpy.mockRestore();
     });
 
-    it('should handle error during db.all', async () => {
-      const error = new Error('db.all failed');
-      mockDb.all.mockImplementationOnce(
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        (_sql: any, _params: any, callback: any) => callback?.(error, []),
-      );
-
-      await expect(logger.getPreviousUserMessages()).rejects.toThrow(
-        'db.all failed',
-      );
+    it('should return empty array if logger not initialized', async () => {
+      const uninitializedLogger = new Logger();
+      const messages = await uninitializedLogger.getPreviousUserMessages();
+      expect(messages).toEqual([]);
+      uninitializedLogger.close();
     });
   });
 
   describe('close', () => {
-    it('should close the database connection', () => {
+    it('should reset logger state', async () => {
+      await logger.logMessage(MessageSenderType.USER, 'A message');
       logger.close();
-      expect(mockDb.close).toHaveBeenCalled();
-    });
-
-    it('should handle database not initialized', () => {
-      const uninitializedLogger = new Logger();
-      // uninitializedLogger.initialize() is not called
-      uninitializedLogger.close();
-      expect(() => uninitializedLogger.close()).not.toThrow();
-    });
-
-    it('should handle error during db.close', () => {
-      const error = new Error('db.close failed');
-      mockDb.close.mockImplementationOnce((callback: (error: Error) => void) =>
-        callback?.(error),
-      );
-      const consoleErrorSpy = vi
-        .spyOn(console, 'error')
+      const consoleDebugSpy = vi
+        .spyOn(console, 'debug')
         .mockImplementation(() => {});
-
-      logger.close();
-      expect(consoleErrorSpy).toHaveBeenCalledWith(
-        'Error closing database:',
-        error.message,
+      await logger.logMessage(MessageSenderType.USER, 'Another message');
+      expect(consoleDebugSpy).toHaveBeenCalledWith(
+        'Logger not initialized or session ID missing. Cannot log message.',
       );
-      consoleErrorSpy.mockRestore();
+      const messages = await logger.getPreviousUserMessages();
+      expect(messages).toEqual([]);
+      expect(logger['initialized']).toBe(false);
+      expect(logger['logFilePath']).toBeUndefined();
+      expect(logger['logs']).toEqual([]);
+      expect(logger['sessionId']).toBeUndefined();
+      expect(logger['messageId']).toBe(0);
+      consoleDebugSpy.mockRestore();
     });
   });
 });
diff --git a/packages/server/src/core/logger.ts b/packages/server/src/core/logger.ts
index d12d4240..feb16944 100644
--- a/packages/server/src/core/logger.ts
+++ b/packages/server/src/core/logger.ts
@@ -5,127 +5,235 @@
  */
 
 import path from 'node:path';
-import sqlite3 from 'sqlite3';
 import { promises as fs } from 'node:fs';
 
 const GEMINI_DIR = '.gemini';
-const DB_NAME = 'logs.db';
-const CREATE_TABLE_SQL = `
-CREATE TABLE IF NOT EXISTS messages (
-    session_id INTEGER,
-    message_id INTEGER,
-    timestamp TEXT,
-    type TEXT,
-    message TEXT
-);`;
+const LOG_FILE_NAME = 'logs.json';
 
 export enum MessageSenderType {
   USER = 'user',
 }
 
+export interface LogEntry {
+  sessionId: number;
+  messageId: number;
+  timestamp: string;
+  type: MessageSenderType;
+  message: string;
+}
+
 export class Logger {
-  private db: sqlite3.Database | undefined;
+  private logFilePath: string | undefined;
   private sessionId: number | undefined;
-  private messageId: number | undefined;
+  private messageId = 0; // Instance-specific counter for the next messageId
+  private initialized = false;
+  private logs: LogEntry[] = []; // In-memory cache, ideally reflects the last known state of the file
 
   constructor() {}
 
-  async initialize(): Promise<void> {
-    if (this.db) {
-      return;
+  private async _readLogFile(): Promise<LogEntry[]> {
+    if (!this.logFilePath) {
+      throw new Error('Log file path not set during read attempt.');
+    }
+    try {
+      const fileContent = await fs.readFile(this.logFilePath, 'utf-8');
+      const parsedLogs = JSON.parse(fileContent);
+      if (!Array.isArray(parsedLogs)) {
+        console.debug(
+          `Log file at ${this.logFilePath} is not a valid JSON array. Starting with empty logs.`,
+        );
+        await this._backupCorruptedLogFile('malformed_array');
+        return [];
+      }
+      return parsedLogs.filter(
+        (entry) =>
+          typeof entry.sessionId === 'number' &&
+          typeof entry.messageId === 'number' &&
+          typeof entry.timestamp === 'string' &&
+          typeof entry.type === 'string' &&
+          typeof entry.message === 'string',
+      ) as LogEntry[];
+    } catch (error) {
+      const nodeError = error as NodeJS.ErrnoException;
+      if (nodeError.code === 'ENOENT') {
+        return [];
+      }
+      if (error instanceof SyntaxError) {
+        console.debug(
+          `Invalid JSON in log file ${this.logFilePath}. Backing up and starting fresh.`,
+          error,
+        );
+        await this._backupCorruptedLogFile('invalid_json');
+        return [];
+      }
+      console.debug(
+        `Failed to read or parse log file ${this.logFilePath}:`,
+        error,
+      );
+      throw error;
     }
-
-    this.sessionId = Math.floor(Date.now() / 1000);
-    this.messageId = 0;
-
-    // Could be cleaner if our sqlite package supported promises.
-    return new Promise((resolve, reject) => {
-      const DB_DIR = path.resolve(process.cwd(), GEMINI_DIR);
-      const DB_PATH = path.join(DB_DIR, DB_NAME);
-      fs.mkdir(DB_DIR, { recursive: true })
-        .then(() => {
-          this.db = new sqlite3.Database(
-            DB_PATH,
-            sqlite3.OPEN_READWRITE |
-              sqlite3.OPEN_CREATE |
-              sqlite3.OPEN_FULLMUTEX,
-            (err: Error | null) => {
-              if (err) {
-                reject(err);
-              }
-
-              // Read and execute the SQL script in create_tables.sql
-              this.db?.exec(CREATE_TABLE_SQL, (err: Error | null) => {
-                if (err) {
-                  this.db?.close();
-                  reject(err);
-                }
-                resolve();
-              });
-            },
-          );
-        })
-        .catch(reject);
-    });
   }
 
-  /**
-   * Get list of previous user inputs sorted most recent first.
-   * @returns list of messages.
-   */
-  async getPreviousUserMessages(): Promise<string[]> {
-    if (!this.db) {
-      console.error('Database not initialized.');
-      return [];
+  private async _backupCorruptedLogFile(reason: string): Promise<void> {
+    if (!this.logFilePath) return;
+    const backupPath = `${this.logFilePath}.${reason}.${Date.now()}.bak`;
+    try {
+      await fs.rename(this.logFilePath, backupPath);
+      console.debug(`Backed up corrupted log file to ${backupPath}`);
+    } catch (_backupError) {
+      // If rename fails (e.g. file doesn't exist), no need to log an error here as the primary error (e.g. invalid JSON) is already handled.
+    }
+  }
+
+  async initialize(): Promise<void> {
+    if (this.initialized) {
+      return;
+    }
+    this.sessionId = Math.floor(Date.now() / 1000);
+    const geminiDir = path.resolve(process.cwd(), GEMINI_DIR);
+    this.logFilePath = path.join(geminiDir, LOG_FILE_NAME);
+
+    try {
+      await fs.mkdir(geminiDir, { recursive: true });
+      let fileExisted = true;
+      try {
+        await fs.access(this.logFilePath);
+      } catch (_e) {
+        fileExisted = false;
+      }
+      this.logs = await this._readLogFile();
+      if (!fileExisted && this.logs.length === 0) {
+        await fs.writeFile(this.logFilePath, '[]', 'utf-8');
+      }
+      const sessionLogs = this.logs.filter(
+        (entry) => entry.sessionId === this.sessionId,
+      );
+      this.messageId =
+        sessionLogs.length > 0
+          ? Math.max(...sessionLogs.map((entry) => entry.messageId)) + 1
+          : 0;
+      this.initialized = true;
+    } catch (err) {
+      console.error('Failed to initialize logger:', err);
+      this.initialized = false;
+    }
+  }
+
+  private async _updateLogFile(
+    entryToAppend: LogEntry,
+  ): Promise<LogEntry | null> {
+    if (!this.logFilePath) {
+      console.debug('Log file path not set. Cannot persist log entry.');
+      throw new Error('Log file path not set during update attempt.');
     }
 
-    return new Promise((resolve, reject) => {
-      // Most recent messages first
-      const query = `SELECT message FROM messages 
-      WHERE type = '${MessageSenderType.USER}'
-      ORDER BY session_id DESC, message_id DESC`;
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      this.db!.all(query, [], (err: Error | null, rows: any[]) => {
-        if (err) {
-          reject(err);
-        } else {
-          resolve(rows.map((row) => row.message));
-        }
-      });
-    });
+    let currentLogsOnDisk: LogEntry[];
+    try {
+      currentLogsOnDisk = await this._readLogFile();
+    } catch (readError) {
+      console.debug(
+        'Critical error reading log file before append:',
+        readError,
+      );
+      throw readError;
+    }
+
+    // Determine the correct messageId for the new entry based on current disk state for its session
+    const sessionLogsOnDisk = currentLogsOnDisk.filter(
+      (e) => e.sessionId === entryToAppend.sessionId,
+    );
+    const nextMessageIdForSession =
+      sessionLogsOnDisk.length > 0
+        ? Math.max(...sessionLogsOnDisk.map((e) => e.messageId)) + 1
+        : 0;
+
+    // Update the messageId of the entry we are about to append
+    entryToAppend.messageId = nextMessageIdForSession;
+
+    // Check if this entry (same session, same *recalculated* messageId, same content) might already exist
+    // This is a stricter check for true duplicates if multiple instances try to log the exact same thing
+    // at the exact same calculated messageId slot.
+    const entryExists = currentLogsOnDisk.some(
+      (e) =>
+        e.sessionId === entryToAppend.sessionId &&
+        e.messageId === entryToAppend.messageId &&
+        e.timestamp === entryToAppend.timestamp && // Timestamps are good for distinguishing
+        e.message === entryToAppend.message,
+    );
+
+    if (entryExists) {
+      console.debug(
+        `Duplicate log entry detected and skipped: session ${entryToAppend.sessionId}, messageId ${entryToAppend.messageId}`,
+      );
+      this.logs = currentLogsOnDisk; // Ensure in-memory is synced with disk
+      return null; // Indicate that no new entry was actually added
+    }
+
+    currentLogsOnDisk.push(entryToAppend);
+
+    try {
+      await fs.writeFile(
+        this.logFilePath,
+        JSON.stringify(currentLogsOnDisk, null, 2),
+        'utf-8',
+      );
+      this.logs = currentLogsOnDisk;
+      return entryToAppend; // Return the successfully appended entry
+    } catch (error) {
+      console.debug('Error writing to log file:', error);
+      throw error;
+    }
+  }
+
+  async getPreviousUserMessages(): Promise<string[]> {
+    if (!this.initialized) return [];
+    return this.logs
+      .filter((entry) => entry.type === MessageSenderType.USER)
+      .sort((a, b) => {
+        if (b.sessionId !== a.sessionId) return b.sessionId - a.sessionId;
+        const dateA = new Date(a.timestamp).getTime();
+        const dateB = new Date(b.timestamp).getTime();
+        if (dateB !== dateA) return dateB - dateA;
+        return b.messageId - a.messageId;
+      })
+      .map((entry) => entry.message);
   }
 
   async logMessage(type: MessageSenderType, message: string): Promise<void> {
-    if (!this.db) {
-      console.error('Database not initialized.');
+    if (!this.initialized || this.sessionId === undefined) {
+      console.debug(
+        'Logger not initialized or session ID missing. Cannot log message.',
+      );
       return;
     }
 
-    return new Promise((resolve, reject) => {
-      const query = `INSERT INTO messages (session_id, message_id, type, message, timestamp) VALUES (?, ?, ?, ?, datetime('now'))`;
-      this.messageId = this.messageId! + 1;
-      this.db!.run(
-        query,
-        [this.sessionId || 0, this.messageId - 1, type, message],
-        (err: Error | null) => {
-          if (err) {
-            reject(err);
-          } else {
-            resolve();
-          }
-        },
-      );
-    });
+    // The messageId used here is the instance's idea of the next ID.
+    // _updateLogFile will verify and potentially recalculate based on the file's actual state.
+    const newEntryObject: LogEntry = {
+      sessionId: this.sessionId,
+      messageId: this.messageId, // This will be recalculated in _updateLogFile
+      type,
+      message,
+      timestamp: new Date().toISOString(),
+    };
+
+    try {
+      const writtenEntry = await this._updateLogFile(newEntryObject);
+      if (writtenEntry) {
+        // If an entry was actually written (not a duplicate skip),
+        // then this instance can increment its idea of the next messageId for this session.
+        this.messageId = writtenEntry.messageId + 1;
+      }
+    } catch (_error) {
+      // Error already logged by _updateLogFile or _readLogFile
+    }
   }
 
   close(): void {
-    if (this.db) {
-      this.db.close((err: Error | null) => {
-        if (err) {
-          console.error('Error closing database:', err.message);
-        }
-      });
-      this.db = undefined;
-    }
+    this.initialized = false;
+    this.logFilePath = undefined;
+    this.logs = [];
+    this.sessionId = undefined;
+    this.messageId = 0;
   }
 }