Enhance README with Docker and env variable instructions

[sylwia-budzynska]

Added instructions for running taskflows with Docker and environment variable setup.

[Copilot]

Pull request overview

This PR enhances the README.md with clearer instructions for running taskflows using Docker and setting up environment variables. The changes reorganize the content to prioritize the recommended Docker-based approach and provide a concrete example command.

• Restructured documentation to lead with the recommended Docker script approach
• Added explicit instructions for creating required directories and .env file configuration
• Included a practical example command for running a taskflow

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[Copilot]

Pull request overview

Copilot reviewed 1 out of 1 changed files in this pull request and generated 1 comment.

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[sylwia-budzynska]

Suggested change

The recommended way of running the taskflows in this repo is by creating a codespace, and running the script [`run_seclab_agent.sh`](https://github.com/GitHubSecurityLab/seclab-taskflows/blob/main/src/run_seclab_agent.sh) to run a docker container of the `seclab-taskflow-agent` as outlined [here](https://github.com/GitHubSecurityLab/seclab-taskflow-agent/tree/main?tab=readme-ov-file#deploying-from-docker). Note that this script needs to be run from the `src` directory, and the `.env` file with the environment variables for the custom MCP servers to store data needs to be in the same directory.

The recommended way of running the taskflows in this repo is either locally or by creating a codespace, and then running the script [`run_seclab_agent.sh`](https://github.com/GitHubSecurityLab/seclab-taskflows/blob/main/src/run_seclab_agent.sh) to run a docker container of the `seclab-taskflow-agent` as outlined [here](https://github.com/GitHubSecurityLab/seclab-taskflow-agent/tree/main?tab=readme-ov-file#deploying-from-docker). Note that this script needs to be run from the `src` directory, and the `.env` file with the environment variables for the custom MCP servers to store data needs to be in the same directory.

[sylwia-budzynska]

@p- @kevinbackhouse please see my comment.

In this case, we mention that the codespace option exists, so users are aware of it.

[sylwia-budzynska]

For reference, I proposed this docs improvement based off @p- 's comment on Slack that we might want to add a sentence that you should set the output folders when running in Docker. I added that and additional setup guidelines. Later, @p- shared in a DM that we might not want to suggest that using a codespace is the recommended way of running the taskflows.

@p- @kevinbackhouse Could you review and provide suggestions (it would be best with direct code suggestions rather than comments) on how you think the docs should be worded, so we can agree on a common solution?

[Copilot]

Pull request overview

Copilot reviewed 1 out of 1 changed files in this pull request and generated 1 comment.

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[Copilot]

Pull request overview

Copilot reviewed 1 out of 1 changed files in this pull request and generated 1 comment.

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