missing dependencies deduplication with jsr when using both package.json and deno.json causes resolution issues

[lowlighter]

Version: deno 2.1.4

If you have the same dependency specified in both deno.json/package.json, then it shouldn't be added to the packageJson of the deno lockfile.

This causes resolution issues in some case (e.g. deployctl): Error: The deployment failed: npm package '@jsr/std__assert' does not exist..

// deno.jsonc
{ 
  "imports": {
      "@std/assert": "jsr:@std/assert@^1.0.9"
  }
}

// package.json
{
  "dependencies": {
    "@std/assert": "npm:@jsr/std__assert@^1.0.9"
  }
}

// deno.lock
{
  "specifiers": {
    "jsr:@std/assert@1": "1.0.9",
    "jsr:@std/assert@^1.0.9": "1.0.9",
  },
  "packageJson": {
    "dependencies": [
      "npm:@jsr/std__assert@^1.0.9",
    ]
  }
}