design: align SPM-Kit with the Pharos visual system

[kegouro]

Summary

Reconstructs the SPM-Kit documentation visual system so the portal belongs clearly to the Pharos family while preserving SPM-Kit as a distinct scientific-software identity.

Main changes

• establishes Pharos as the parent identity and SPM-Kit as the scientific instrument;
• replaces the globally dominant teal/Fathom chrome with warm black, ivory and amber;
• reserves teal and related signal colors for scientific data and plots;
• replaces the global Fathom identity with the canonical Pharos/SPM-Kit hierarchy;
• unifies heroes, buttons, cards, statuses, navigation and evidence-level components;
• aligns theory, user manual, ecosystem pages and the embedded PDF reader;
• adds accessible dark/light color contracts and responsive behavior;
• preserves the existing component banners and scientific content;
• hardens the PDF reader to the packaged local manual;
• adds visual-system governance and CI checks;
• preserves compatibility routes for historical evidence URLs.

Verification

• MkDocs strict build
• documentation synchronization checks
• visual-system contract checks
• internal-link validation
• dark/light contrast validation
• case-sensitive route build
• accessibility and keyboard checks
• embedded 19-page PDF reader checks
• responsive browser matrix at 1440, 1280, 1024, 768, 430, 390 and 360 px
• 112/112 final browser scenarios passed
• Python test suite previously reported 253 passed and 26 expected skips
• git diff --check

Scientific-content scope

This PR is primarily a visual-system and documentation-shell reconstruction. It does not broaden scientific validation claims or replace the existing theory, manual, provenance or evidence content.

Authorship

SPM-Kit remains independently designed and developed by José Labarca Baeza.