[Bug]: Could not locate the bindings file error during deployment

### Problem description

I had the same error locally before enabling node_modules directory: nodeModulesDir: auto + "--allow-scripts" installation flag fixed the problem locally.

error: The deployment failed: UNCAUGHT_EXCEPTION

Error: Could not locate the bindings file. Tried:
→ /node_modules/.deno/sqlite3@5.1.7/node_modules/sqlite3/build/node_sqlite3.node
→ /node_modules/.deno/sqlite3@5.1.7/node_modules/sqlite3/build/Debug/node_sqlite3.node
→ /node_modules/.deno/sqlite3@5.1.7/node_modules/sqlite3/build/Release/node_sqlite3.node
→ /node_modules/.deno/sqlite3@5.1.7/node_modules/sqlite3/out/Debug/node_sqlite3.node
→ /node_modules/.deno/sqlite3@5.1.7/node_modules/sqlite3/Debug/node_sqlite3.node
→ /node_modules/.deno/sqlite3@5.1.7/node_modules/sqlite3/out/Release/node_sqlite3.node
→ /node_modules/.deno/sqlite3@5.1.7/node_modules/sqlite3/Release/node_sqlite3.node
→ /node_modules/.deno/sqlite3@5.1.7/node_modules/sqlite3/build/default/node_sqlite3.node
→ /node_modules/.deno/sqlite3@5.1.7/node_modules/sqlite3/compiled/20.11.1/linux/x64/node_sqlite3.node
→ /node_modules/.deno/sqlite3@5.1.7/node_modules/sqlite3/addon-build/release/install-root/node_sqlite3.node
→ /node_modules/.deno/sqlite3@5.1.7/node_modules/sqlite3/addon-build/debug/install-root/node_sqlite3.node
→ /node_modules/.deno/sqlite3@5.1.7/node_modules/sqlite3/addon-build/default/install-root/node_sqlite3.node
→ /node_modules/.deno/sqlite3@5.1.7/node_modules/sqlite3/lib/binding/node-v108-linux-x64/node_sqlite3.node
at bindings (file:///node_modules/.deno/bindings@1.5.0/node_modules/bindings/bindings.js:126:9)
at Object. (file:///node_modules/.deno/sqlite3@5.1.7/node_modules/sqlite3/lib/sqlite3-binding.js:1:282)
at Object. (file:///node_modules/.deno/sqlite3@5.1.7/node_modules/sqlite3/lib/sqlite3-binding.js:3:4)
at Module._compile (node:module:745:34)
at loadMaybeCjs (node:module:770:10)
at Object.Module._extensions..js (node:module:755:12)
at Module.load (node:module:662:32)
at Function.Module._load (node:module:534:12)
at Module.require (node:module:681:19)
at require (node:module:812:16)

### Steps to reproduce

deno add npm:sqlite3@^5.1.7
add nodeModulesDir: auto
deployctl deploy --allow-scripts --project= --entrypoint="src/main.ts"

### Expected behavior

"nodeModulesDir: auto" in deno.json fixes binding issues

### Environment

_No response_

### Possible solution

_No response_

### Additional context

_No response_

Start by reproducing the deployment with deno add npm:sqlite3@^5.1.7, nodeModulesDir: auto in deno.json, and the deployctl command targeting src/main.ts. Compare the result with and without --allow-scripts and verify that deployment succeeds and the sqlite3 binding loads. The issue does not name a source file or test, so investigation will require tracing the deployment configuration and native dependency handling.

Written by the indexing model from the issue text.