How can I make an automation to use a workspace(repository) by default?

I don't think it will...the automation server might be able to if explicitly instructed but I'm not sure. It would be a good idea if that doesn't work.

If you tell the automation what repo, it should work, there is a repo field for the automation that will cline it You could also explicitly add it as a step or the agents.md file could have it

repo meaning repo url and that will automatically know that it needs to clone it?=

yea, the automation have a field for repos: here is mine:

{
  "name": "Jira Bug to PR - KAN Task to PR",
  "preset": "prompt",
  "prompt_file": "prompt.md",
  "trigger": {
    "type": "event",
    "source": "jira-direct",
    "on": "jira:issue_created",
    "filter": "issue.fields.project.key == '${JIRA_DEMO_PROJECT_KEY}' && issue.fields.issuetype.name == 'Task' && !contains(issue.fields.labels, 'sidekick-v2')"
  },
  "repos": [
    {
      "url": "${GITHUB_DEMO_REPO_URL}",
      "ref": "main"
    }
  ],
  "timeout": 900,
  "model": "Bedrock-Claude-Sonnet-4-5-fast"
}

Thanks Both