[IF-Env] Generates incorrect package.json when there is also node-modules inside the folder

[MariamKhalatova]

Description of the Error

When running if-env from a folder, where also exists node-modules, the generated package.json file contains all dependencies from node-modules

Expected Behaviour

Package.json should contain only necessary dependencies, and the ones from node-modules should not be included

Actual Behavior

Dependencies from node-modules are included into the package.json file. This happens both when running from inside if and outside if.

Steps to Reproduce

1. Have node-modules folder with the appropriate dependencies inside it.
2. Run if-env ( the below command is used in case of running from outside of if.
   npm run --prefix=./if if-env -- -m manifests/testing/testing.yaml --cwd

Manifest File That Generated the Error

Testing.yaml

description: >-
  a pipeline that does arbitrary calculations using our generic arithmetic
  builtins
tags: null
initialize:
  plugins:
    teads-curve:
      path: '@grnsft/if-unofficial-plugins'
      method: TeadsCurve
      global-config:
        interpolation: spline
    sum:
      path: builtin
      method: Sum
      global-config:
        input-parameters:
          - cpu/energy
          - network/energy
        output-parameter: energy-sum
    coefficient:
      path: builtin
      method: Coefficient
      global-config:
        input-parameter: energy
        coefficient: 2
        output-parameter: energy-doubled
    multiply:
      path: builtin
      method: Multiply
      global-config:
        input-parameters:
          - cpu/utilization
          - duration
        output-parameter: cpu-times-duration
  outputs:
    - yaml
execution:
  command: >-
    /Users/mariamkhalatova/.npm/_npx/1bf7c3c15bf47d04/node_modules/.bin/ts-node
    /Users/mariamkhalatova/Projects/UK/if/src/index.ts -m
    manifests/testing/generics.yml -o
    /Users/mariamkhalatova/Projects/UK/if/manifests/testing
  environment:
    if-version: 0.4.0
    os: macOS
    os-version: '13.2'
    node-version: 18.14.2
    date-time: 2024-06-23T17:26:28.567Z (UTC)
    dependencies:
      - '@babel/core@7.22.10'
      - '@babel/preset-typescript@7.23.3'
      - '@commitlint/cli@18.6.0'
      - '@commitlint/config-conventional@18.6.0'
      - '@grnsft/if-core@0.0.7'
      - '@grnsft/if-plugins@v0.3.2 extraneous -> file:../../../../if-models'
      - >-
        @grnsft/if-unofficial-plugins@v0.3.1 extraneous ->
        file:../../../../if-unofficial-models
      - '@jest/globals@29.7.0'
      - '@types/jest@29.5.8'
      - '@types/js-yaml@4.0.9'
      - '@types/luxon@3.4.2'
      - '@types/node@20.9.0'
      - axios-mock-adapter@1.22.0
      - axios@1.7.2
      - cross-env@7.0.3
      - csv-parse@5.5.6
      - csv-stringify@6.4.6
      - fixpack@4.0.0
      - gts@5.2.0
      - husky@8.0.3
      - jest@29.7.0
      - js-yaml@4.1.0
      - lint-staged@15.2.2
      - luxon@3.4.4
      - release-it@16.3.0
      - rimraf@5.0.5
      - ts-command-line-args@2.5.1
      - ts-jest@29.1.1
      - typescript-cubic-spline@1.0.1
      - typescript@5.2.2
      - winston@3.11.0
      - zod@3.22.4
  status: success
tree:
  children:
    child-1:
      pipeline:
        - teads-curve
        - sum
        - coefficient
        - multiply
      config: null
      defaults:
        cpu/thermal-design-power: 100
      inputs:
        - timestamp: '2023-12-12T00:00:00.000Z'
          cloud/instance-type: A1
          cloud/region: uk-west
          duration: 1
          cpu/utilization: 50
          network/energy: 10
          energy: 5
        - timestamp: '2023-12-12T00:00:01.000Z'
          duration: 5
          cpu/utilization: 20
          cloud/instance-type: A1
          cloud/region: uk-west
          network/energy: 10
          energy: 5
        - timestamp: '2023-12-12T00:00:06.000Z'
          duration: 7
          cpu/utilization: 15
          cloud/instance-type: A1
          cloud/region: uk-west
          network/energy: 10
          energy: 5
        - timestamp: '2023-12-12T00:00:13.000Z'
          duration: 30
          cloud/instance-type: A1
          cloud/region: uk-west
          cpu/utilization: 15
          network/energy: 10
          energy: 5
      outputs:
        - timestamp: '2023-12-12T00:00:00.000Z'
          cloud/instance-type: A1
          cloud/region: uk-west
          duration: 1
          cpu/utilization: 50
          network/energy: 10
          energy: 5
          cpu/thermal-design-power: 100
          cpu/energy: 0.000020833333333333333
          energy-sum: 10.000020833333334
          energy-doubled: 10
          cpu-times-duration: 50
        - timestamp: '2023-12-12T00:00:01.000Z'
          duration: 5
          cpu/utilization: 20
          cloud/instance-type: A1
          cloud/region: uk-west
          network/energy: 10
          energy: 5
          cpu/thermal-design-power: 100
          cpu/energy: 0.00006635035569105689
          energy-sum: 10.000066350355691
          energy-doubled: 10
          cpu-times-duration: 100
        - timestamp: '2023-12-12T00:00:06.000Z'
          duration: 7
          cpu/utilization: 15
          cloud/instance-type: A1
          cloud/region: uk-west
          network/energy: 10
          energy: 5
          cpu/thermal-design-power: 100
          cpu/energy: 0.00007870368606029811
          energy-sum: 10.00007870368606
          energy-doubled: 10
          cpu-times-duration: 105
        - timestamp: '2023-12-12T00:00:13.000Z'
          duration: 30
          cloud/instance-type: A1
          cloud/region: uk-west
          cpu/utilization: 15
          network/energy: 10
          energy: 5
          cpu/thermal-design-power: 100
          cpu/energy: 0.0003373015116869919
          energy-sum: 10.000337301511687
          energy-doubled: 10
          cpu-times-duration: 450