chore: apply AEOS repository standards scaffolding

[aadil96]

Summary

• Add AEOS repository standards to the dotfiles repo
• BRANCHING.md — Branch naming conventions (feat/fix/chore/docs/refactor)
• docs/operations/quality-gates.md — Pre-merge quality checklist
• .github/workflows/ci.yml — GitHub Actions CI (ShellCheck, markdownlint, test)
• docs/ structure — architecture, workflows, operations, references directories

Test Plan

• CI should run on PR creation
• ShellCheck should pass
• markdownlint should pass

Related

• autonomous-engineering-os PR #1 — AEOS repo standards scaffolding

[what-the-diff]

PR Summary

• Established Continuous Integration Pipeline
  The team has established a continuous integration system, this will automatically check new code additions to ensure they do not adversely affect the existing project. This includes automated linting and tests that were set up in the .github/workflows/ci.yml.

• Ignored Unnecessary Files
  Our ".gitignore" file, which essentially tells us what local files we do not want to upload to the repository, has been updated. Now it will overlook directories and patterns such as runtime/, .aeos/, and *.log.

• Defined Branching Protocol
  A new file named BRANCHING.md has been added which stipulates our branching strategy. This involves set policies, naming conventions, and certain operations, which are not allowed on branches.

• Initiated Architecture Documentation
  The team has taken a step towards clearer code structure by implementing docs/architecture/README.md. This will provide others insight into the layout of the system's different components.

• Introduced Operations and Quality Control Documentation
  To streamline the merging process, new documents docs/operations/README.md and quality-gates.md have been added. These define the operational processes and quality checks that should be passed before merging changes to the main branch.

• Improved Workflow and References Documentation
  With the goal of providing better comprehension of the codebase, docs/references/README.md and docs/workflows/README.md have been added. These help to explain the references and workflow patterns.