docs: add project to CLI examples

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What does this PR do?

Updates the README CLI examples to include the required project field for project-scoped tool calls.

The previous examples showed commands such as search_graph, trace_path, query_graph, and --raw search_graph without a project value, which can lead to project not found or not indexed errors when users copy the examples directly.

This PR also adds a short note telling users to run list_projects first and use the returned project name as the project value.

Closes #945.

Checklist

• Every commit is signed off (git commit -s) — required, CI rejects unsigned commits (DCO, see CONTRIBUTING.md)
• Tests pass locally (make -f Makefile.cbm test) — not run; docs-only change
• Lint passes locally (make -f Makefile.cbm lint-ci) — not run; docs-only change
• New behavior is covered by a test — not applicable; README-only documentation fix

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Looks like ci-ok failed only because test / test-windows (windows-latest, CLANG64, x86_64) was cancelled. This PR only changes docs/Markdown, and the product-change detector reports product=false.

Could maintainers rerun the cancelled Windows job or rerun failed jobs?