…ory to use relative links for local files, instead of plain text. This improves the readability and navigability of the documentation.

The following files were updated:
- AGENTS.md
- CONTRIBUTING.md
- .github/PULL_REQUEST_TEMPLATE.md
- .github/SECURITY.md
- docs/docker.md
- docs/github-codespaces.md
- docs/github-workflows.md
- docs/standard-files.md

This work was done in response to a request to update all markdown files. The process is not yet complete, and there are still some markdown files that need to be checked for plain text file path references. The work was submitted at the user's request.