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.

server/tsconfig.json

@@ -3,6 +3,10 @@
     "target": "ES2022",
     "module": "NodeNext",
     "moduleResolution": "NodeNext",
+    "baseUrl": "./src",
+    "paths": {
+      "@/*": ["./*"]
+    },
     "rootDir": "./src",
     "outDir": "./dist",
     "strict": true,