Simplify Makefile / Dockerfile interactions using docker-compose.yml

[ahouseholder]

This PR refactors our use of make and docker to use docker-compose, which simplifies the process for building and running container images. This will be useful as a foundation for future architectures where we need to spin up more containers for microservices, as we begin to address things like #655.

CoPilot Summary

This pull request refactors the project's Docker setup to simplify workflows and improve maintainability. Key changes include replacing individual Makefile Docker commands with docker-compose commands, reorganizing Docker-related files into a dedicated docker directory, and updating documentation to reflect these changes.

Docker Setup Refactoring:

• Makefile Changes: Removed individual Docker build and run targets (dockerbuild_test, dockerrun_test, dockerbuild_docs, dockerrun_docs) in favor of consolidated docker-compose commands (docker_test, docs, up, down). Updated help text to reflect the new commands.
• Dockerfile Updates: Moved Dockerfile to a dedicated docker directory and updated paths for requirements and application files to reflect the new directory structure.
• docker-compose.yml Addition: Added a docker-compose.yml file to define services (base, dependencies, test, docs) and streamline Docker workflows.

Documentation Updates:

• Docker Directory Description: Added a new section to README.md describing the docker directory and its purpose for managing Docker configurations.
• Updated Commands: Replaced outdated Docker commands with docker-compose equivalents in sections for running the documentation server (make docs) and tests (make docker_test). Adjusted port mapping details for the docs server. [1] [2]

[Copilot]

Pull Request Overview

This PR refactors our Docker setup by replacing individual Makefile Docker targets with a docker‑compose based workflow for improved simplicity and maintainability.

• Consolidates Docker image build/run commands into a docker-compose configuration.
• Reorganizes Docker-related files into a dedicated docker directory and updates the documentation accordingly.

Reviewed Changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 1 comment.

File	Description
docker/docker-compose.yml	New docker-compose file defining services for base, dependencies, test, and docs.
docker/Dockerfile	Adjusted COPY commands to reflect the new directory structure.
README.md	Updated instructions and examples to use docker-compose commands.
Makefile	Removed individual Docker targets; added targets for tests, docs, up, and down using docker-compose.

Comments suppressed due to low confidence (1)

Makefile:20

• [nitpick] Clarify in the help message that the 'test' target runs tests locally while the 'docker_test' target runs tests in a Docker container to avoid potential confusion.

pushd $(DOCKER_DIR) && docker-compose run --rm test