Fix test target and integration opt-in

[marcpaterno]

Description

This PR does some improvement of the Makefile to streamline the development workflow.

Add --runintegration pytest option so that tests marked with the integration marker are skipped by default, consistent with the existing --runslow and --example behavior. Update the test-integration Makefile target to pass this flag.

Remove the test-coverage target and merge its coverage- reporting behavior directly into the test target, making coverage collection the default for all test runs.

Update all documentation (CONTRIBUTING.md, Makefile help text, copilot-instructions.md, testing_protocol, and auto_testing instructions) to reflect these changes.

Type of change

• Refactoring, only of Makefile and related documentation and testing configuration,

Checklist:

The following checklist will make sure that you are following the code style and
guidelines of the project as described in the
contributing page.

• I have run bash pre-commit-check and fixed any issues
• I have added tests that prove my fix is effective or that my feature works
• I have made corresponding changes to the documentation
• I have 100% test coverage for my changes (please check this after the CI system has verified the coverage)

[Copilot]

Pull request overview

This PR refines the developer testing workflow by making integration tests opt-in via a new pytest flag and by making coverage collection the default behavior of make test.

Changes:

• Add a --runintegration pytest option and skip @pytest.mark.integration tests unless explicitly enabled.
• Remove the test-coverage Makefile target and fold coverage reporting into the default test target.
• Update CONTRIBUTING documentation to reflect the updated targets/workflows.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.

File	Description
tests/conftest.py	Adds --runintegration and default-skipping behavior for integration-marked tests.
Makefile	Makes make test generate coverage by default and updates test-integration to opt in to integration tests.
CONTRIBUTING.md	Updates workflow docs/diagrams to include test-all and reflect coverage-default test runs.

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[Copilot]

Mermaid labels generally don’t interpret escaped \n sequences; they tend to render literally. Since the rest of this file uses <br/> for line breaks in Mermaid node labels, consider replacing \n in this label with <br/> to ensure consistent rendering in the docs.

Suggested change

	test-all --> test["make test\n(+coverage)"]
	test-all --> test["make test<br/>(+coverage)"]

[Copilot]

In the test target, the coverage JSON filename later echoed to the user is hard-coded as coverage.json, but the report is generated at $(COVERAGE_JSON) (which can include COVERAGE_ID). Please update the echoed filename to use the variable so it matches the actual artifact name.