Do not set permissions for jobs with GITHUB_TOKEN in job level env variable

[varunsh-coder]

There is an error condition to not set permissions for jobs with GITHUB_TOKEN in step level env variable

secure-repo/remediation/workflow/permissions/permissions.go

Line 35 in d61982f

const errorSecretInRunStepEnvVariable = "KnownIssue-2: Jobs with run steps that use token in environment variable are not supported"

But if env variable is set at job level, the code sets token permissions. These may be incorrect as the specific logic to determine the permissions is not known.

Here is a test workflow

name: Job level env
on:
  pull_request:
    branches: [main]

jobs:
  Lint:
    env:
      GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
    runs-on: ubuntu-latest
    steps:
      
      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
      - name: some step that uses token
        run: |
          npm ci

[varunsh-coder]

Done