chore(deps): update npm packages

- Updated package versions using `bun update` respecting the semver ranges
- Migrated `biome.json` config according to the new Biome version
- Removed unnecessary temp log files from git tree
- Successfully verified the application stability by running validation suite

Co-authored-by: YunosukeYoshino <26004836+YunosukeYoshino@users.noreply.github.com>

Author: google-labs-jules[bot]

biome.json

@@ -1,5 +1,5 @@
 {
-  "$schema": "https://biomejs.dev/schemas/2.4.14/schema.json",
+  "$schema": "https://biomejs.dev/schemas/2.4.16/schema.json",
   "vcs": {
     "enabled": true,
     "clientKind": "git",