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 repository structure by moving scripts from the src/ directory into a dedicated scripts/ directory and updates the main wrapper script to run from the repository root instead of requiring users to change into the src/ directory first.

Changes:

• Moved run_seclab_agent.sh from src/ to scripts/ and updated it to install the package and execute commands from the repo root
• Moved run_audit.sh from src/ to scripts/audit/ and changed it from calling the wrapper script to directly using python -m seclab_taskflow_agent
• Updated README.md documentation to reflect the new script locations and remove the requirement to cd src before running commands

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
src/run_seclab_agent.sh	Removed the old docker wrapper script from the src directory
src/run_audit.sh	Removed the old audit script from the src directory
scripts/run_seclab_agent.sh	Added new docker wrapper script that runs from repo root and installs package before execution
scripts/audit/run_audit.sh	Added new audit script that directly invokes python module instead of calling wrapper
README.md	Updated documentation to reference new script paths and removed instruction to cd into src directory

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[Copilot]

Pull request overview

Copilot reviewed 5 out of 5 changed files in this pull request and generated no new comments.

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[kevinbackhouse]

@p- @m-y-mo : Are you happy with this? It changes the docker workflow, but I think it's an improvement because now you can run the script from the main directory, rather than needing to cd into src.