refactor: restructure db logic and add import alias using tsc-alias

Note: the legacy githubTokensDb migration is not included in this commit.
It's used only in `agents.js` and will be removed in a future commit. We
will directly use credentials repository instead of github tokens repository.

package.json

@@ -27,7 +27,7 @@
     "dev": "concurrently --kill-others \"npm run server\" \"npm run client\"",
     "server:dev": "tsx watch server/src/bootstrap.ts",
     "server": "tsx server/src/bootstrap.ts",
-    "server:build": "tsc -p server/tsconfig.json",
+    "server:build": "tsc -p server/tsconfig.json && tsc-alias -p server/tsconfig.json",
     "server:start": "node server/index.js",
     "client": "vite",
     "build": "vite build",
@@ -116,6 +116,7 @@
     "@commitlint/config-conventional": "^20.4.3",
     "@eslint/js": "^9.39.3",
     "@release-it/conventional-changelog": "^10.0.5",
+    "@types/better-sqlite3": "^7.6.13",
     "@types/cors": "^2.8.19",
     "@types/express": "^5.0.3",
     "@types/node": "^22.19.7",
@@ -141,6 +142,7 @@
     "release-it": "^19.0.5",
     "sharp": "^0.34.2",
     "tailwindcss": "^3.4.0",
+    "tsc-alias": "^1.8.16",
     "tsx": "^4.20.6",
     "typescript": "^5.9.3",
     "typescript-eslint": "^8.56.1",