Consolidate env at repo root

- Move all application env vars to repository-root .env (with .env.example
  as the committed template) and drop the per-app .env.example files.
- Add @code/env subpaths (agent, convex) and consume validated exports
  everywhere instead of reading process.env directly.
- Wire every dev/build/start script to load ../../.env via bun --env-file
  and point vite.config.ts envDir at the repo root.

apps/daemon/package.json

@@ -5,9 +5,9 @@
   "type": "module",
   "module": "src/index.ts",
   "scripts": {
-    "dev": "bun run --watch src/index.ts",
-    "build": "bun build src/index.ts --compile --outfile dist/code-daemon",
-    "start": "./dist/code-daemon",
+    "dev": "bun --env-file=../../.env run --watch src/index.ts",
+    "build": "bun --env-file=../../.env build src/index.ts --compile --outfile dist/code-daemon",
+    "start": "bun --env-file=../../.env ./dist/code-daemon",
     "check-types": "tsc --noEmit"
   },
   "dependencies": {