docs: update security and readme files [skip:ci, skip:test:long-runni…

[omid-aignostics]

• Fixed typos in SECURITY.md: "Dependendabot" → "Dependabot", "encouraring" → "encouraging"
• Fixed duplicate list markers in SECURITY.md section 2: (a), (a), (d) → (a), (b), (c)
• Fixed list item rendering in SECURITY.md by adding blank lines between items in all 4 sections so they render on separate lines in the HTML output
• Improved mermaid diagram readability in docs/partials/README_main.md: dark theme, white text and arrows, 18px font
• Made mermaid diagram use full page width via custom CSS (docs/source/_static/custom.css)
• Restored accidentally removed MCP Server documentation from docs/partials/README_main.md and docs/partials/README_glossary.md
• Regenerated docs artifacts (README.md, API_REFERENCE_v1.md, CLI_REFERENCE.md, ATTRIBUTIONS.md, openapi_v1.yaml) by running make docs

[Copilot]

Pull request overview

This PR updates documentation presentation (Mermaid diagram theming + Sphinx CSS inclusion), refreshes some generated/auxiliary docs (OpenAPI YAML, CLI reference, attributions), and applies minor import ordering changes in the platform module/tests.

Changes:

• Add Sphinx custom CSS and Mermaid init configuration to improve diagram rendering/visibility.
• Reformat/update several documentation artifacts (SECURITY.md, OpenAPI spec YAML, CLI reference, attributions) and remove the README’s MCP Server section.
• Reorder platform constants imports in platform settings code and tests.

Reviewed changes

Copilot reviewed 10 out of 12 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tests/aignostics/platform/settings_test.py	Reorders imported platform constants.
src/aignostics/platform/_settings.py	Reorders imported constants used by platform settings.
src/aignostics/platform/init.py	Reorders exports/imports of platform constants (also touches __all__).
docs/source/conf.py	Includes custom.css in Sphinx HTML build.
docs/source/_static/custom.css	Adds CSS to allow Mermaid diagrams to use full width.
docs/source/_static/openapi_v1.yaml	Reformats OpenAPI YAML content (currently appears to introduce invalid YAML).
docs/partials/README_main.md	Adds Mermaid init/theme configuration for the main README partial.
SECURITY.md	Formatting fixes and a typo correction.
README.md	Adds Mermaid init/theme configuration; removes MCP Server documentation and MCP glossary entry.
CLI_REFERENCE.md	Adds mcp command docs and updates some CLI help text formatting.
ATTRIBUTIONS.md	Updates dependency attributions/license text (large regen/update).

Comments suppressed due to low confidence (1)

src/aignostics/platform/init.py:121

• __all__ contains many duplicated entries (e.g. DEFAULT_CPU_PROVISIONING_MODE, DEFAULT_GPU_PROVISIONING_MODE, DEFAULT_GPU_TYPE, etc.). This is harmless at runtime but makes the public surface noisy/confusing for users and for generated docs. Please deduplicate the list so each export appears once.

    "DEFAULT_CPU_PROVISIONING_MODE",
    "DEFAULT_CPU_PROVISIONING_MODE",
    "DEFAULT_FLEX_START_MAX_RUN_DURATION_MINUTES",
    "DEFAULT_GPU_PROVISIONING_MODE",
    "DEFAULT_GPU_PROVISIONING_MODE",
    "DEFAULT_GPU_TYPE",
    "DEFAULT_GPU_TYPE",
    "DEFAULT_MAX_GPUS_PER_SLIDE",

[Copilot]

Pull request overview

Copilot reviewed 11 out of 13 changed files in this pull request and generated no new comments.