Site + Architecture Redesign: new design system, component architecture, and page rework

[bencap]

Full visual and structural overhaul of the MaveDB UI, introducing a cohesive design system and modern component architecture while preserving all existing functionality.

Design system foundation

• Tailwind CSS + PrimeVue Aura theme with custom sage/orange/danger palettes and CSS design tokens
• New layout shell: MvLayout, MvNavBar, MvFooter, MvPageHeader
• Reusable primitives: MvEmptyState, MvLoader, MvStatusMessage, MvRowActionMenu, MvMetadataLine, MvCollectionStrip, MvBadge, etc.

Component reorganization

• Moved feature components into domain subdirectories: score-set/, calibration/, collection/, dashboard/, variant/
• Renamed common components with Mv* prefix for consistency
• Extracted form sections (ExperimentFields, ScoreSetFields, TargetFields, etc.) shared between creator wizard and editor card layouts
• Deleted old component copies at original locations

Typed API layer

• New mavedb modules replacing inline axios calls: experiments.ts, score-sets.ts, calibrations.ts, collections.ts, permissions.ts, users.ts, variants.ts, access-keys.ts, orcid.ts
• New clingen module for ClinGen allele lookups
• Barrel export via @/api/mavedb

Composables

• use-dataset-permissions — reactive permission checks replacing per-page authorization boilerplate
• use-score-set-downloads — shared download logic for score set data files
• use-variant-coordinates — stateless HGVS coordinate resolution utilities
• use-autocomplete — lightweight search/autocomplete replacing useItems() for form fields
• use-publication-identifiers, use-validation-errors, use-calibration-editor, use-dashboard, and others

Page redesigns

• All screen components (ScoreSetView, ExperimentView, ExperimentSetView, DashboardView, SearchView, SettingsScreen, CollectionView, VariantScreen, etc.) rewritten with new design language, MvPageHeader, and typed API calls
• New MvDashboard* tab components with filtering, sorting, and status summaries
• Redesigned search with MvSearchFilters chip-based filtering

Documentation (supersedes #601)

• Migrated docs from Sphinx to MkDocs Material with integrated build pipeline
• Updated all Copilot instruction files to reflect new architecture

Removed dead code

• Deleted public/prototype/ static HTML pages used during early design exploration
• Removed old component copies superseded by reorganized versions
• Before merge

Three items need to be wired before this is production-ready:

• Recently published endpoint — The homepage "Recently Published" section uses stub data (home.ts). Wire to the real API once the endpoint is available.
• Calibrations endpoint — calibrations.ts includes a stub for /me/calibrations. Wire to the real endpoint when the API adds it.
• Activity notification bell — MvNavBar has a notification bell with placeholder activities. Gate the bell icon behind a feature flag or hide it until the backend activity feed endpoint is created.

In addition, various TODOs were sprinkled throughout this change set that we should formalize as issues and link prior to merging.