Redesign the research website and agent documentation

[GiggleLiu]

The public website now presents Problem Reductions as infrastructure for autonomous research. Visitors can explore exact problem variants and reduction evidence, then use short task guides to run the CLI or direct an agent. The dark palette retains the original project logo; distracting uppercase labels have been removed.

The atlas is generated from registry exports and distinguishes implemented capabilities from the autonomous research goal. It includes searchable problem families, variant-specific connections, reduction contracts, source/API/test links, and an interactive independent-set / vertex-cover example.

Documentation is reorganized into 37 focused pages (median about 160 words): agent workflows first, followed by CLI tasks, Rust examples, and internals. Each page has direct Markdown access with expanded code includes. Existing guide URLs remain available, and old section links route to their new task pages. The reading layout preserves mdBook search, code copying, and mobile navigation.

A real six-command CLI recording discovers an MIS → ILP route, creates a five-vertex cycle, saves a reduction bundle, recovers a source solution, evaluates it, and cross-checks the optimum by exhaustive search. All commands exited 0. The demo includes copyable commands, expected results, a downloadable cast, and a self-contained offline player with autoplay disabled. Stale installation, factoring flags, solver claims, and Rust path APIs were corrected against the current implementation.

The documentation build combines the product site, guides, Markdown exports, API, and PDF in book/. Local preview and recording maintenance instructions are in docs/website/README.md.

Validation

• 15 website browser checks passed: search, filters, variants, deep links, clipboard, example interaction, docs/API links, and 320–1440px layouts.
• 10 documentation checks passed on mdBook 0.4.37 (deployment) and 0.5.2: navigation, search, code copying, Markdown includes and local links, old section redirects, mobile controls, offline playback, and CLI replay.
• All 37 guides were checked at 320px and 390px with no page overflow or uncaught browser errors.
• All 529 atlas variant/reduction records rendered; implementation, API, and test targets were audited.
• Automated WCAG A/AA scans found no violations on four product views and four key documentation pages.
• CLI examples were executed; the first Rust program, direct ILP reduction, and dynamic path execution snippets were compiled and run successfully.
• make doc, make paper, reduction-graph JavaScript tests, Python syntax checks, and whitespace checks passed. Rustdoc emits 49 existing warnings.
• Original logo geometry and lettering are preserved; only palette colors change during the build.

Previews

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 98.00%. Comparing base (cb54ea0) to head (0612a68).

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1139   +/-   ##
=======================================
  Coverage   98.00%   98.00%           
=======================================
  Files        1044     1044           
  Lines      107366   107366           
=======================================
  Hits       105228   105228           
  Misses       2138     2138           

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