fix: bundle @mcpedia/* deps in nix build, fix runtime module resolution

Replace --external approach (which failed because @mcpedia/* workspace
packages couldn't resolve their npm deps like ioredis/bullmq at runtime)
with full bundling. The key fixes:

1. Bundle all code into a single JS file (no --external for @mcpedia/*)
   - This inlines @mcpedia/core, @mcpedia/queue, ioredis, bullmq, etc.
   - Produces ~2.6MB self-contained binary, no node_modules needed

2. Fix .bun cache symlink issues in nix sandbox:
   - After bun install, copy .bun cache with cp -rL to dereference
     relative symlinks that break in nix build sandbox
   - This was the root cause of 'File not found msgpackr-extract' errors

3. Only @mcpedia/config, embeddings, types kept external (lightweight,
   no npm deps) - resolved via packages/ source symlinks at runtime

All 3 services (api, mcp, worker) now build and run successfully in nix store.
Resolves CI failure run 32474463114 ('Cannot find module @mcpedia/core').

flake.lock

@@ -20,16 +20,16 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1787172299,
-        "narHash": "sha256-PShzS87awOlE5XWkxUGBd/58/F+AtE2ZMgFffKj4r8s=",
+        "lastModified": 1787135253,
+        "narHash": "sha256-RD2kNWCG+Bjo6h+JVjWVNntZs2GtRoeY2xHjts/FNkA=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "07e1d92cdc0ed416cfa11ff3ca40d17e61cfba7a",
+        "rev": "ffb3c9b700e759be2ef13237c9d8f953b32a1e46",
         "type": "github"
       },
       "original": {
         "owner": "NixOS",
-        "ref": "nixpkgs-unstable",
+        "ref": "nixos-unstable",
         "repo": "nixpkgs",
         "type": "github"
       }