panu.js

const fs = require('fs')
const data = require('./source.json')

function writeFile(filename, content) {
  fs.writeFileSync(filename, content)
}

function removeNulls (list) {
  return list.filter(item => !!item)
}

writeFile('first.json', JSON.stringify(data.glossary))
writeFile('second.json', JSON.stringify(removeNulls(data.items)))

source.json

{
  "glossary": {
    "title": "example glossary",
    "GlossDiv": {
      "title": "S",
      "GlossList": {
        "GlossEntry": {
          "ID": "SGML",
          "SortAs": "SGML",
          "GlossTerm": "Standard Generalized Markup Language",
          "Acronym": "SGML",
          "Abbrev": "ISO 8879:1986",
          "GlossDef": {
            "para": "A meta-markup language, used to create markup languages such as DocBook.",
            "GlossSeeAlso": ["GML", "XML"]
          },
          "GlossSee": "markup"
        }
      }
    }
  },
  "items": [
    {"id": "Open"},
    {"id": "OpenNew", "label": "Open New"},
    null,
    {"id": "ZoomIn", "label": "Zoom In"},
    {"id": "ZoomOut", "label": "Zoom Out"},
    {"id": "OriginalView", "label": "Original View"},
    null,
    {"id": "Quality"},
    {"id": "Pause"},
    {"id": "Mute"},
    null,
    {"id": "Find", "label": "Find..."},
    {"id": "FindAgain", "label": "Find Again"},
    {"id": "Copy"},
    {"id": "CopyAgain", "label": "Copy Again"},
    {"id": "CopySVG", "label": "Copy SVG"},
    {"id": "ViewSVG", "label": "View SVG"},
    {"id": "ViewSource", "label": "View Source"},
    {"id": "SaveAs", "label": "Save As"},
    null,
    {"id": "Help"},
    {"id": "About", "label": "About Adobe CVG Viewer..."}
  ]
}