fix(docs): fix broken API reference page on ReadTheDocs

[omid-aignostics]

Summary

• yaml.dump default width=80 wrapped long strings at column 80,
  causing some words to land at column 0 in openapi_v1.yaml
• YAML parsers interpret bare words at column 0 as new keys, making
  the file invalid
• Widdershins silently failed to parse it and output garbage markdown
  into API_REFERENCE_v1.md, breaking the rendered page on ReadTheDocs

Fix

• Pass width=float("inf") to yaml.dump to disable line wrapping
• Use print() instead of console.print() to avoid Rich adding a
  second layer of wrapping on top

Test plan

• Verify aignostics system openapi --output-format=yaml produces valid YAML
• Verify https://aignostics.readthedocs.io/en/latest/api_reference_v1.html renders correctly after merge

🤖 Generated with Claude Code

[Copilot]

Pull request overview

This PR fixes broken ReadTheDocs rendering of the v1 API reference by ensuring the generated OpenAPI YAML is valid (no line-wrapping that breaks YAML parsing), and regenerates the derived API reference Markdown.

Changes:

• Update aignostics system openapi --output-format=yaml to emit unwrapped YAML to stdout.
• Regenerate docs/source/_static/openapi_v1.yaml and API_REFERENCE_v1.md from the corrected OpenAPI YAML.
• Minor docs maintenance updates (RST include formatting, CLI reference output, misc formatting/whitespace).

Reviewed changes

Copilot reviewed 5 out of 16 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
src/aignostics/system/_cli.py	Adjust YAML dumping/printing for OpenAPI export to prevent wrap-induced invalid YAML.
docs/source/security.rst	Minor include directive formatting.
docs/source/release-notes.rst	Minor include directive formatting.
docs/source/platform_overview.rst	Minor include directive formatting.
docs/source/operational_excellence.rst	Minor include directive formatting.
docs/source/license.rst	Minor include directive formatting.
docs/source/glossary.rst	Minor include directive formatting.
docs/source/cli_reference.rst	Minor include directive formatting.
docs/source/attributions.rst	Minor include directive formatting.
docs/source/api_reference_v1.rst	Minor include directive formatting.
docs/source/_static/openapi_v1.yaml	Regenerated OpenAPI YAML with long strings no longer wrapped into invalid YAML.
README.md	Adds an MCP Server section to the interface overview.
CLI_REFERENCE.md	Regenerated CLI reference output (notably GPU default now A100).
CHANGELOG.md	Removes trailing blank lines.
API_REFERENCE_v1.md	Regenerated API reference output from OpenAPI via Widdershins.
.license-types-allowed	Formatting/indentation fix for license entry list.

[Copilot]

README.md is generated from docs partials during the docs build (see noxfile.py generate_readme). Direct edits here are likely to be overwritten the next time docs are regenerated; please apply this change in the appropriate docs/partials/README*.md source instead and re-generate README.md.

[Copilot]

API_REFERENCE_v1.md appears to be committed as raw Widdershins output (HTML headings/anchors still present). The repo’s docs generation pipeline post-processes Widdershins output (see noxfile.py _generate_api_reference) and would produce a different, cleaned Markdown file; please regenerate via the standard docs task (or adjust the post-processing if the new raw format is intended) so the committed artifact matches the documented generation process.