Move scripts to their own directory

[kevinbackhouse]

This PR does two things:

1. Modify the run_seclab_agent.sh script so that you run it from the main directory of the repo, rather than having to first cd into the src directory. This is currently a weird discrepancy between the docker experience and the codespaces experience which I want to fix. The main change is that the script now runs pip install -q -e /app so that python's importlib knows where to find the files.
2. Move run_seclab_agent.sh and run_audit.sh into a new scripts directory.

After this change, you can run the run_audit.sh script in docker like this:

./scripts/run_seclab_agent.sh ./scripts/audit/run_audit.sh github/cmark-gfm

Or, you can run it in codespaces (or on bare metal) like this:

/scripts/audit/run_audit.sh github/cmark-gfm

[Copilot]

Pull request overview

This PR reorganizes the helper scripts for running the SecLab taskflows and aligns the Docker-based workflow with running from the repository root. It moves the scripts into a dedicated scripts hierarchy and updates how the agent is started so Python can import the project via an editable install.

Changes:

• Remove src/run_seclab_agent.sh and reintroduce it as scripts/run_seclab_agent.sh, now running Docker with an editable install of /app and a bind-mounted logs directory.
• Remove src/run_audit.sh and add scripts/audit/run_audit.sh, which runs the audit taskflow via python -m seclab_taskflow_agent instead of the Docker wrapper.
• Update the overall layout so scripts live under scripts/ and can be invoked from the repo root, aligning the Docker and Codespaces usage patterns (though the PR description and existing docs still reference the old src/ paths).

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 2 comments.

File	Description
src/run_seclab_agent.sh	Removes the old Docker wrapper script that had to be invoked from src/.
src/run_audit.sh	Removes the previous audit helper that delegated to run_seclab_agent.sh in src/.
scripts/run_seclab_agent.sh	New Docker wrapper in scripts/ that mounts the repo at /app, mounts ./logs into /root/.local, and runs pip install -q -e /app before executing the provided command.
scripts/audit/run_audit.sh	New audit script under scripts/audit/ that validates the repo argument and runs the audit taskflow via python -m seclab_taskflow_agent.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

Pull request overview

Copilot reviewed 4 out of 4 changed files in this pull request and generated 4 comments.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

Pull request overview

Copilot reviewed 4 out of 4 changed files in this pull request and generated 2 comments.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

The script has been moved from src/run_seclab_agent.sh to scripts/run_seclab_agent.sh, but the top-level README and other docs (for example README.md lines 7–9 and src/seclab_taskflows/mcp_servers/codeql_python/README.md line 29) still reference the old location and assume it is run from src. Please update those docs and examples to point at the new scripts/ path and root-level .env/data locations so users don’t follow outdated instructions.

[Copilot]

The PR description suggests running the audit script directly in Codespaces as /scripts/audit/run_audit.sh github/cmark-gfm, but the script is added at scripts/audit/run_audit.sh within the repo, so the correct usage from the repo root would be ./scripts/audit/run_audit.sh github/cmark-gfm (or similar). Please align the description and any user-facing examples with the actual relative path so users don’t try to call a non-existent absolute /scripts/... path.