npm - @iowarp/clio-coder - Versions diffs - 0.3.0 - Mend

@iowarp/clio-coder 0.3.0

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Files changed (226) hide show

package/CHANGELOG.md +407 -0
package/CODE_OF_CONDUCT.md +21 -0
package/CONTRIBUTING.md +224 -0
package/LICENSE +202 -0
package/NOTICE +9 -0
package/README.md +798 -0
package/SECURITY.md +72 -0
package/assets/clio-coder-logo-128.webp +0 -0
package/damage-control-rules.yaml +419 -0
package/dist/acp-UMLFVA3F.js +92 -0
package/dist/agents-Q4MYPMUW.js +91 -0
package/dist/auth-O6HYIJ6J.js +521 -0
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package/docs/exit-codes-and-output.md +74 -0
package/docs/extensions-and-sharing.md +306 -0
package/docs/fleet-demo-runbook.md +179 -0
package/docs/fleet-dispatch.md +591 -0
package/docs/glossary.md +75 -0
package/docs/html/agents_blueprint.html +936 -0
package/docs/html/alcf_blueprint.html +324 -0
package/docs/html/architecture_blueprint.html +850 -0
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package/docs/html/config_knobs_audit_blueprint.html +178 -0
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package/docs/html/memory_blueprint.html +699 -0
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package/docs/html/skills_blueprint.html +671 -0
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package/docs/html/tool_usage_blueprint.html +350 -0
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package/docs/html/validation_blueprint.html +961 -0
package/docs/html/worker_dispatch_blueprint.html +231 -0
package/docs/installation-and-lifecycle.md +308 -0
package/docs/middleware-and-components.md +148 -0
package/docs/model-catalog.md +189 -0
package/docs/observability.md +233 -0
package/docs/proactive-memory.md +452 -0
package/docs/prompt-envelope-and-tools.md +142 -0
package/docs/provider-adapter-cookbook.md +148 -0
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package/docs/scientific-validation.md +105 -0
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package/docs/worker-dispatch-mechanics.md +242 -0
package/package.json +132 -0
package/skills/README.md +408 -0
package/skills/git/commit-crafting/SKILL.md +79 -0
package/skills/git/commit-crafting/evals.md +92 -0
package/skills/git/create-pr/SKILL.md +116 -0
package/skills/git/create-pr/evals.md +114 -0
package/skills/git/investigate-issue/SKILL.md +139 -0
package/skills/git/investigate-issue/evals.md +94 -0
package/skills/git/resolve-merge-conflicts/SKILL.md +96 -0
package/skills/git/resolve-merge-conflicts/evals.md +58 -0
package/skills/git/review-changes/SKILL.md +103 -0
package/skills/git/review-changes/evals.md +85 -0
package/skills/git/worktree-create/SKILL.md +92 -0
package/skills/git/worktree-create/evals.md +97 -0
package/skills/git/worktree-create/references/worktree-setup.md +66 -0
package/skills/git/worktree-merge/SKILL.md +95 -0
package/skills/git/worktree-merge/evals.md +114 -0
package/skills/skill-marketplace.json +261 -0
package/skills/workflow/cut-it/SKILL.md +86 -0
package/skills/workflow/cut-it/evals.md +42 -0
package/src/domains/agents/builtins/architect.md +33 -0
package/src/domains/agents/builtins/coder.md +31 -0
package/src/domains/agents/builtins/context-bootstrap.md +38 -0
package/src/domains/agents/builtins/debugger.md +30 -0
package/src/domains/agents/builtins/documenter.md +31 -0
package/src/domains/agents/builtins/git-master.md +30 -0
package/src/domains/agents/builtins/provenance.md +30 -0
package/src/domains/agents/builtins/researcher.md +71 -0
package/src/domains/agents/builtins/scout.md +42 -0
package/src/domains/agents/builtins/tester.md +31 -0
package/src/domains/agents/builtins/verifier.md +30 -0
package/src/domains/agents/builtins/wiki-writer.md +41 -0
package/src/domains/agents/fleets/build-review.md +34 -0
package/src/domains/agents/fleets/build-test.md +35 -0
package/src/domains/agents/fleets/sdlc.md +86 -0
package/src/domains/prompts/fragments/identity/clio-worker.md +11 -0
package/src/domains/prompts/fragments/identity/clio.md +26 -0
package/src/domains/prompts/fragments/operating/contract.md +64 -0
package/src/domains/prompts/fragments/safety/auto-edit.md +14 -0
package/src/domains/prompts/fragments/safety/full-auto.md +14 -0
package/src/domains/prompts/fragments/safety/read-only.md +13 -0
package/src/domains/prompts/fragments/safety/suggest.md +13 -0
package/src/domains/prompts/fragments/wiki/page.md +75 -0
package/src/domains/prompts/fragments/wiki/plan.md +48 -0
package/src/domains/providers/models/cloud-models/alcf.yaml +40 -0
package/src/domains/providers/models/local-models/clio-local-coding-targets.yaml +993 -0

package/docs/html/index.html ADDED Viewed

@@ -0,0 +1,919 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+  <meta charset="UTF-8">
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  <title>Clio Coder Documentation Hub (v0.3.0)</title>
+  <link rel="stylesheet" href="shared.css">
+  <style>
+    /* Unique homepage layouts */
+    .hub-header {
+      text-align: center;
+      margin-bottom: 3.5rem;
+      padding-bottom: 2rem;
+      border-bottom: 1px solid rgba(255, 255, 255, 0.05);
+    }
+    .hub-logo {
+      display: inline-flex;
+      align-items: center;
+      justify-content: center;
+      width: 80px;
+      height: 80px;
+      background: rgba(255, 255, 255, 0.02);
+      border: 1px solid var(--border-card);
+      border-radius: 24px;
+      margin-bottom: 1.5rem;
+      position: relative;
+      box-shadow: var(--shadow-glow);
+    }
+    .hub-logo::after {
+      content: '';
+      position: absolute;
+      inset: -2px;
+      border-radius: 26px;
+      background: var(--gradient-main);
+      z-index: -1;
+      opacity: 0.3;
+      filter: blur(8px);
+    }
+    .hub-logo svg {
+      width: 48px;
+      height: 48px;
+    }
+    .hub-title {
+      font-size: 2.8rem;
+      font-weight: 800;
+      letter-spacing: -0.05em;
+      margin-bottom: 0.75rem;
+      background: linear-gradient(to right, #ffffff, #c7d2fe, var(--color-cyan));
+      -webkit-background-clip: text;
+      -webkit-text-fill-color: transparent;
+    }
+    .subtitle {
+      font-size: 1.15rem;
+      color: var(--text-muted);
+      max-width: 750px;
+      margin: 0 auto 1.5rem auto;
+    }
+    /* Category Filter Grid */
+    .filter-section {
+      margin-bottom: 2rem;
+    }
+    .filter-tags {
+      display: flex;
+      flex-wrap: wrap;
+      gap: 0.5rem;
+      justify-content: center;
+      margin-bottom: 2rem;
+    }
+    .filter-tag {
+      background: rgba(255, 255, 255, 0.03);
+      border: 1px solid var(--border-card);
+      color: var(--text-muted);
+      padding: 0.4rem 1rem;
+      border-radius: 9999px;
+      font-size: 0.825rem;
+      cursor: pointer;
+      font-weight: 600;
+      transition: all 0.2s;
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+    .filter-tag:hover {
+      background: rgba(255, 255, 255, 0.08);
+      color: var(--text-main);
+    }
+    .filter-tag.active {
+      background: var(--color-cyan);
+      color: #090d16;
+      border-color: transparent;
+      box-shadow: 0 0 12px rgba(0, 212, 219, 0.3);
+    }
+    /* Operator Journeys Panel */
+    .journeys-panel {
+      margin-bottom: 3.5rem;
+    }
+    .journeys-grid {
+      display: grid;
+      grid-template-columns: repeat(auto-fit, minmax(240px, 1fr));
+      gap: 1.25rem;
+    }
+    .journey-card {
+      background: rgba(13, 20, 38, 0.35);
+      border: 1px solid rgba(255,255,255,0.05);
+      border-radius: 12px;
+      padding: 1.25rem;
+      transition: all 0.2s;
+    }
+    .journey-card:hover {
+      border-color: rgba(var(--color-orange-rgb), 0.35);
+      background: rgba(13, 20, 38, 0.5);
+    }
+    .journey-title {
+      font-size: 0.9rem;
+      text-transform: uppercase;
+      font-weight: 700;
+      letter-spacing: 0.05em;
+      color: var(--color-orange);
+      margin-bottom: 0.5rem;
+      display: flex;
+      align-items: center;
+      gap: 0.4rem;
+    }
+    .journey-links {
+      display: flex;
+      flex-direction: column;
+      gap: 0.35rem;
+      font-size: 0.85rem;
+    }
+    .journey-links a {
+      color: var(--text-muted);
+      text-decoration: none;
+      transition: color 0.15s;
+    }
+    .journey-links a:hover {
+      color: #fff;
+      text-decoration: underline;
+    }
+    /* Hub Grid */
+    .hub-grid {
+      display: grid;
+      grid-template-columns: repeat(auto-fill, minmax(320px, 1fr));
+      gap: 1.5rem;
+    }
+    /* Document Cards */
+    .doc-card {
+      background: var(--bg-card);
+      border: 1px solid var(--border-card);
+      border-radius: 14px;
+      padding: 1.5rem;
+      text-decoration: none;
+      color: inherit;
+      transition: all 0.25s cubic-bezier(0.4, 0, 0.2, 1);
+      display: flex;
+      flex-direction: column;
+      height: 100%;
+      position: relative;
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+    .doc-card:hover {
+      background: var(--bg-card-hover);
+      border-color: var(--border-card-hover);
+      transform: translateY(-4px);
+      box-shadow: 0 10px 25px rgba(0, 0, 0, 0.4), 0 0 15px rgba(255, 126, 41, 0.1);
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+    .doc-card.flagship:hover {
+      border-color: var(--color-orange);
+      box-shadow: 0 10px 25px rgba(0, 0, 0, 0.4), 0 0 15px rgba(255, 126, 41, 0.15);
+    }
+    .doc-card.flagship::before {
+      content: '';
+      position: absolute;
+      top: 0;
+      left: 0;
+      width: 100%;
+      height: 3px;
+      background: var(--gradient-main);
+      border-radius: 14px 14px 0 0;
+    }
+    .card-top {
+      display: flex;
+      justify-content: space-between;
+      align-items: flex-start;
+      margin-bottom: 0.75rem;
+    }
+    .card-title {
+      font-size: 1.15rem;
+      font-weight: 700;
+      color: #fff;
+      transition: color 0.2s;
+    }
+    .doc-card:hover .card-title {
+      color: var(--color-orange);
+    }
+    .card-badge {
+      font-size: 0.7rem;
+      padding: 0.2rem 0.5rem;
+      border-radius: 4px;
+      font-weight: 700;
+      text-transform: uppercase;
+    }
+    .badge-flagship {
+      background: rgba(255, 126, 41, 0.1);
+      border: 1px solid rgba(255, 126, 41, 0.3);
+      color: var(--color-orange);
+    }
+    .badge-ref {
+      background: rgba(16, 185, 129, 0.08);
+      border: 1px solid rgba(16, 185, 129, 0.25);
+      color: var(--color-emerald);
+    }
+    .badge-internal {
+      background: rgba(245, 158, 11, 0.08);
+      border: 1px solid rgba(245, 158, 11, 0.25);
+      color: var(--color-amber);
+    }
+    .badge-markdown {
+      background: rgba(99, 102, 241, 0.12);
+      border: 1px solid rgba(99, 102, 241, 0.35);
+      color: #a5b4fc;
+    }
+    .card-desc {
+      font-size: 0.875rem;
+      color: var(--text-muted);
+      margin-bottom: 1.25rem;
+      flex-grow: 1;
+    }
+    .card-footer {
+      border-top: 1px solid rgba(255, 255, 255, 0.05);
+      padding-top: 0.75rem;
+      display: flex;
+      justify-content: space-between;
+      align-items: center;
+      font-size: 0.75rem;
+      color: var(--text-dim);
+    }
+    .card-footer .path {
+      font-family: var(--font-mono);
+      overflow: hidden;
+      text-overflow: ellipsis;
+      white-space: nowrap;
+      max-width: 60%;
+    }
+    .card-footer .feature {
+      color: var(--color-orange);
+      font-weight: 600;
+    }
+  </style>
+</head>
+<body>
+  <div class="container">
+    <div class="hub-header">
+      <div class="hub-logo">
+        <svg viewBox="0 0 24 24" fill="none" xmlns="http://www.w3.org/2000/svg">
+          <path d="M12 2L2 7L12 12L22 7L12 2Z" stroke="url(#logoGrad)" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"/>
+          <path d="M2 17L12 22L22 17" stroke="url(#logoGrad)" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"/>
+          <path d="M2 12L12 17L22 12" stroke="url(#logoGrad)" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"/>
+          <defs>
+            <linearGradient id="logoGrad" x1="2" y1="2" x2="22" y2="22" gradientUnits="userSpaceOnUse">
+              <stop stop-color="#00d4db" />
+              <stop offset="1" stop-color="#ff7e29" />
+            </linearGradient>
+          </defs>
+        </svg>
+      </div>
+      <h1 class="hub-title">Clio Coder Documentation Hub</h1>
+      <p class="subtitle">Interactive technical blueprints and specifications for IOWarp's terminal-first agentic computing orchestrator</p>
+      <div class="meta-badges">
+        <span class="meta-badge version">
+          <svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><title>Icon</title><circle cx="12" cy="12" r="10"></circle><polyline points="12 6 12 12 16 14"></polyline></svg>
+          v0.3.0
+        </span>
+        <span class="meta-badge" style="border-color: rgba(255,255,255,0.08); color: var(--text-muted);">
+          CLI command: <code style="color: var(--color-orange); margin-left: 0.35rem;">clio-coder docs [topic]</code>
+        </span>
+      </div>
+    </div>
+    <!-- Search Controls -->
+    <div class="glass-card" style="padding: 1.25rem; margin-bottom: 2rem;">
+      <div class="form-group" style="margin-bottom: 0;">
+        <input type="text" id="searchDocs" placeholder="Search blueprints, keys, file paths, interactive features..." oninput="filterCards()" style="padding: 0.85rem 1.25rem; font-size: 1rem; border-radius: 10px;">
+      </div>
+    </div>
+    <!-- Filter Tags -->
+    <div class="filter-section">
+      <div class="filter-tags" id="filterTags">
+        <button type="button" class="filter-tag active" onclick="setCategory('all')">All blueprints</button>
+        <button type="button" class="filter-tag" onclick="setCategory('start')">Start &amp; Configure</button>
+        <button type="button" class="filter-tag" onclick="setCategory('operate')">Operate &amp; Tools</button>
+        <button type="button" class="filter-tag" onclick="setCategory('safety')">Safety &amp; Context</button>
+        <button type="button" class="filter-tag" onclick="setCategory('fleet')">Agents &amp; Fleet</button>
+        <button type="button" class="filter-tag" onclick="setCategory('obs')">Observability &amp; Trace</button>
+        <button type="button" class="filter-tag" onclick="setCategory('models')">Models &amp; Providers</button>
+        <button type="button" class="filter-tag" onclick="setCategory('skills')">Extensions &amp; Skills</button>
+        <button type="button" class="filter-tag" onclick="setCategory('validation')">Validation, Evals &amp; Soak</button>
+        <button type="button" class="filter-tag" onclick="setCategory('reference')">Reference &amp; Arch</button>
+        <button type="button" class="filter-tag" onclick="setCategory('internal')">Internal/Historical</button>
+      </div>
+    </div>
+    <!-- Operator Journeys -->
+    <div class="glass-card journeys-panel">
+      <h2 style="font-size: 1.1rem; border-bottom: 1px solid rgba(255,255,255,0.05); padding-bottom: 0.5rem; margin-bottom: 1rem; text-transform: uppercase; color: var(--text-dim);">
+        Learning Path &amp; Operator Journeys
+      </h2>
+      <div class="journeys-grid">
+        <div class="journey-card">
+          <div class="journey-title">
+            <svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2"><title>Icon</title><polygon points="5 3 19 12 5 21 5 3"></polygon></svg>
+            1. Install &amp; Configure
+          </div>
+          <div class="journey-links">
+            <a href="lifecycle_blueprint.html">1. Installation &amp; Directory Layout</a>
+            <a href="configuration_blueprint.html">2. Configuration Settings Profile</a>
+            <a href="alcf_blueprint.html">3. HPC / ALCF Inference Setup</a>
+            <a href="environment_blueprint.html">4. Environment Variables Matrix</a>
+          </div>
+        </div>
+        <div class="journey-card">
+          <div class="journey-title">
+            <svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2"><title>Icon</title><rect x="3" y="11" width="18" height="11" rx="2" ry="2"></rect><path d="M7 11V7a5 5 0 0 1 10 0v4"></path></svg>
+            2. Run Tasks &amp; Tools
+          </div>
+          <div class="journey-links">
+            <a href="commands_blueprint.html">1. Commands &amp; Headless Flags</a>
+            <a href="tools_blueprint.html">2. Seven-Plane Tool Surface</a>
+            <a href="tool_usage_blueprint.html">3. Detailed Tool Usage Reference</a>
+            <a href="tui_design_blueprint.html">4. TUI Design &amp; Glyphs</a>
+          </div>
+        </div>
+        <div class="journey-card">
+          <div class="journey-title">
+            <svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2"><title>Icon</title><path d="M12 22s8-4 8-10V5l-8-3-8 3v7c0 6 8 10 8 10z"></path></svg>
+            3. Safety &amp; Context
+          </div>
+          <div class="journey-links">
+            <a href="safety_blueprint.html">1. Safety Postures &amp; Autonomy</a>
+            <a href="context_blueprint.html">2. Context Window &amp; Compaction</a>
+            <a href="validation_blueprint.html">3. Scientific Validation Contracts</a>
+            <a href="architecture_blueprint.html">4. Architecture Boundary Rules</a>
+          </div>
+        </div>
+        <div class="journey-card">
+          <div class="journey-title">
+            <svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2"><title>Icon</title><path d="M17 21v-2a4 4 0 0 0-4-4H5a4 4 0 0 0-4 4v2"></path><circle cx="9" cy="7" r="4"></circle><path d="M23 21v-2a4 4 0 0 0-3-3.87"></path><path d="M16 3.13a4 4 0 0 1 0 7.75"></path></svg>
+            4. Multi-Node &amp; Fleets
+          </div>
+          <div class="journey-links">
+            <a href="fleet_dispatch_blueprint.html">1. Multi-Node SSH Fleet Dispatch</a>
+            <a href="agents_blueprint.html">2. Built-in Agent Recipes</a>
+            <a href="worker_dispatch_blueprint.html">3. Worker Subprocess Mechanics</a>
+          </div>
+        </div>
+        <div class="journey-card">
+          <div class="journey-title">
+            <svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2"><title>Icon</title><circle cx="12" cy="12" r="10"></circle><polyline points="12 6 12 12 16 14"></polyline></svg>
+            5. Measure, Trace &amp; Verify
+          </div>
+          <div class="journey-links">
+            <a href="trace_blueprint.html">1. WAL SQLite Trace Store</a>
+            <a href="soak_blueprint.html">2. Machinery Soak Benchmark</a>
+            <a href="eval_blueprint.html">3. Evaluation Runner &amp; Dual Tokens</a>
+            <a href="observability_blueprint.html">4. Observability &amp; Receipts</a>
+          </div>
+        </div>
+      </div>
+    </div>
+    <!-- Hub Grid -->
+    <main class="hub-grid" id="hubGrid">
+      <!-- Card: Safety Model -->
+      <a href="safety_blueprint.html" class="doc-card flagship" data-categories="safety,start" data-title="Safety Model" data-tags="safety security autonomy block rules gate bash rollback">
+        <div class="card-top">
+          <h3 class="card-title">Safety Model</h3>
+          <span class="card-badge badge-flagship">Core</span>
+        </div>
+        <p class="card-desc">Autonomy dials, safety net rules, default-deny shell constraints, detect-and-rollback write boundaries, and interactive validation loops.</p>
+        <div class="card-footer">
+          <span class="path">safety-model.md</span>
+          <span class="feature">Safety Simulator</span>
+        </div>
+      </a>
+      <!-- Card: Configuration & Targets -->
+      <a href="configuration_blueprint.html" class="doc-card flagship" data-categories="configure,start" data-title="Configuration &amp; Targets" data-tags="config target route settings yaml connection provenance">
+        <div class="card-top">
+          <h3 class="card-title">Configuration &amp; Targets</h3>
+          <span class="card-badge badge-flagship">Core</span>
+        </div>
+        <p class="card-desc">Profile definitions, context-window provenance, settings routing, and interactive validation checkers.</p>
+        <div class="card-footer">
+          <span class="path">configuration-and-targets.md</span>
+          <span class="feature">YAML Validator</span>
+        </div>
+      </a>
+      <!-- Card: Commands & Modes -->
+      <a href="commands_blueprint.html" class="doc-card flagship" data-categories="operate,start" data-title="Commands &amp; Modes" data-tags="commands CLI slash steering keybindings postures session continue json">
+        <div class="card-top">
+          <h3 class="card-title">Commands &amp; Modes</h3>
+          <span class="card-badge badge-flagship">Core</span>
+        </div>
+        <p class="card-desc">CLI flags, headless session continuity (--session/--continue), key steering triggers, slash actions, and operating mode states.</p>
+        <div class="card-footer">
+          <span class="path">commands-and-modes.md</span>
+          <span class="feature">Command Palette</span>
+        </div>
+      </a>
+      <!-- Card: Architecture -->
+      <a href="architecture_blueprint.html" class="doc-card flagship" data-categories="reference,start" data-title="Architecture" data-tags="architecture boundaries rules direction flow domain loader engine worker">
+        <div class="card-top">
+          <h3 class="card-title">Architecture</h3>
+          <span class="card-badge badge-flagship">Core</span>
+        </div>
+        <p class="card-desc">Source layout, 5 enforced boundary rules (dependency direction vs import form), runtime flow, and detect-and-rollback boundaries.</p>
+        <div class="card-footer">
+          <span class="path">architecture.md</span>
+          <span class="feature">Boundary Check</span>
+        </div>
+      </a>
+      <!-- Card: Context Engine -->
+      <a href="context_blueprint.html" class="doc-card" data-categories="safety,context" data-title="Context Engine" data-tags="context window compaction token ledger prime prefix">
+        <div class="card-top">
+          <h3 class="card-title">Context Engine</h3>
+          <span class="card-badge badge-ref">Ref</span>
+        </div>
+        <p class="card-desc">Sliding window mechanics, compaction thresholds, model-driven init, format v3 session enforcement, and prefix cache audits.</p>
+        <div class="card-footer">
+          <span class="path">context-engine.md</span>
+          <span class="feature">Compaction Calc</span>
+        </div>
+      </a>
+      <!-- Card: Prompt Envelope & Tools -->
+      <a href="tools_blueprint.html" class="doc-card" data-categories="safety,operate" data-title="Prompt Envelope &amp; Tools" data-tags="tools envelope registry envelope results truncate adapter">
+        <div class="card-top">
+          <h3 class="card-title">Prompt Envelope &amp; Tools</h3>
+          <span class="card-badge badge-ref">Ref</span>
+        </div>
+        <p class="card-desc">Envelopes structure, twenty tools grouped into seven planes via single agent-tools.ts adapter, observation budgets, and safety checks.</p>
+        <div class="card-footer">
+          <span class="path">prompt-envelope-and-tools.md</span>
+          <span class="feature">Tool Inspector</span>
+        </div>
+      </a>
+      <!-- Card: Installation & Lifecycle -->
+      <a href="lifecycle_blueprint.html" class="doc-card" data-categories="start" data-title="Installation &amp; Lifecycle" data-tags="install update bootstrap directories doctor repair reset permissions">
+        <div class="card-top">
+          <h3 class="card-title">Installation &amp; Lifecycle</h3>
+          <span class="card-badge badge-ref">Ref</span>
+        </div>
+        <p class="card-desc">Source install instructions, configuration directories layouts, permissions matrix (0o600 credentials), validation repair, and reset cleaning.</p>
+        <div class="card-footer">
+          <span class="path">installation-and-lifecycle.md</span>
+          <span class="feature">Command Builder</span>
+        </div>
+      </a>
+      <!-- Card: ALCF Inference Provider -->
+      <a href="alcf_blueprint.html" class="doc-card" data-categories="start,models" data-title="ALCF Inference Provider" data-tags="alcf supercomputer HPC sophia metis globus oauth PKCE">
+        <div class="card-top">
+          <h3 class="card-title">ALCF Inference Provider</h3>
+          <span class="card-badge badge-ref">Ref</span>
+        </div>
+        <p class="card-desc">Argonne National Lab HPC supercomputer access config, Sophia/Metis models, and Globus PKCE authentication flow.</p>
+        <div class="card-footer">
+          <span class="path">alcf-provider.md</span>
+          <span class="feature">OAuth Diagram</span>
+        </div>
+      </a>
+      <!-- Card: Environment Variables -->
+      <a href="environment_blueprint.html" class="doc-card" data-categories="start,reference" data-title="Environment Variables" data-tags="environment env vars knobs overrides debugging path">
+        <div class="card-top">
+          <h3 class="card-title">Environment Variables</h3>
+          <span class="card-badge badge-ref">Ref</span>
+        </div>
+        <p class="card-desc">Comprehensive reference of variables recognized by Clio runtime: settings overrides, directory paths, debug loggers.</p>
+        <div class="card-footer">
+          <span class="path">environment-variables.md</span>
+          <span class="feature">Env Matrix</span>
+        </div>
+      </a>
+      <!-- Card: Tool Usage Reference -->
+      <a href="tool_usage_blueprint.html" class="doc-card" data-categories="operate,reference" data-title="Tool Usage Reference" data-tags="tools details read write edit bash grep dispatch code_nav">
+        <div class="card-top">
+          <h3 class="card-title">Tool Usage Reference</h3>
+          <span class="card-badge badge-ref">Ref</span>
+        </div>
+        <p class="card-desc">In-depth reference for all 19 worker tools including parameters, typical payloads, prepareArguments normalizers, and error examples.</p>
+        <div class="card-footer">
+          <span class="path">tool-usage.md</span>
+          <span class="feature">Tool Atlas</span>
+        </div>
+      </a>
+      <!-- Card: Provider Adapter Cookbook -->
+      <a href="provider_adapter_blueprint.html" class="doc-card" data-categories="models,reference" data-title="Provider Adapter Cookbook" data-tags="provider adapter custom model integration descriptor probe config">
+        <div class="card-top">
+          <h3 class="card-title">Provider Adapter Cookbook</h3>
+          <span class="card-badge badge-ref">Ref</span>
+        </div>
+        <p class="card-desc">Step-by-step instructions for adding custom LLM/inference provider adapters, routing templates, and probe formats.</p>
+        <div class="card-footer">
+          <span class="path">provider-adapter-cookbook.md</span>
+          <span class="feature">Descriptor Builder</span>
+        </div>
+      </a>
+      <!-- Card: Built-in Agents -->
+      <a href="agents_blueprint.html" class="doc-card" data-categories="fleet" data-title="Built-in Agents" data-tags="agents recipes built-ins schemas dispatch catalog context">
+        <div class="card-top">
+          <h3 class="card-title">Built-in Agents</h3>
+          <span class="card-badge badge-ref">Ref</span>
+        </div>
+        <p class="card-desc">Built-in recipes catalog, frontmatter config properties, fleet contract shadowing (.clio-coder/fleets/<name>.md), and custom additions.</p>
+        <div class="card-footer">
+          <span class="path">built-in-agents.md</span>
+          <span class="feature">Recipe Check</span>
+        </div>
+      </a>
+      <!-- Card: Fleet Dispatch -->
+      <a href="fleet_dispatch_blueprint.html" class="doc-card flagship" data-categories="fleet,operate" data-title="Fleet Dispatch" data-tags="fleet dispatch remote ssh doctor capacity leases write boundary loops code steps attestation">
+        <div class="card-top">
+          <h3 class="card-title">Fleet Dispatch</h3>
+          <span class="card-badge badge-flagship">Core</span>
+        </div>
+        <p class="card-desc">Multi-node SSH execution, process-safe capacity leases, Contract v4 per-step write boundaries (detect-and-rollback), bounded loops, deterministic code steps, and worker attestation.</p>
+        <div class="card-footer">
+          <span class="path">fleet-dispatch.md</span>
+          <span class="feature">Fleet Simulator</span>
+        </div>
+      </a>
+      <!-- Card: Trace Store -->
+      <a href="trace_blueprint.html" class="doc-card flagship" data-categories="obs,validation" data-title="Trace Store" data-tags="trace sqlite wal runs phases procs sql subcommands">
+        <div class="card-top">
+          <h3 class="card-title">Trace Store</h3>
+          <span class="card-badge badge-flagship">Core</span>
+        </div>
+        <p class="card-desc">Durable WAL SQLite trace mirror database schema, rowid cursor queries, rebuildability, and the 6 `clio-coder trace` subcommands (runs, phases, tail, procs, sql, ui).</p>
+        <div class="card-footer">
+          <span class="path">trace-store.md</span>
+          <span class="feature">Trace SQL Inspector</span>
+        </div>
+      </a>
+      <!-- Card: Soak Machinery Benchmark -->
+      <a href="soak_blueprint.html" class="doc-card flagship" data-categories="validation,obs" data-title="Soak Machinery Benchmark" data-tags="soak benchmark suites machinery reliability boundary chaos loop">
+        <div class="card-top">
+          <h3 class="card-title">Soak Machinery Benchmark</h3>
+          <span class="card-badge badge-flagship">Core</span>
+        </div>
+        <p class="card-desc">Offline benchmark suite measuring Clio machinery reliability (not model quality): core soak, write boundaries, SIGINT chaos, and loop bound exhaustion.</p>
+        <div class="card-footer">
+          <span class="path">evals-internal.md</span>
+          <span class="feature">Soak Suite Simulator</span>
+        </div>
+      </a>
+      <!-- Card: Evidence & Memory -->
+      <a href="memory_blueprint.html" class="doc-card" data-categories="obs" data-title="Evidence &amp; Memory" data-tags="memory evidence database session audit approval log">
+        <div class="card-top">
+          <h3 class="card-title">Evidence &amp; Memory</h3>
+          <span class="card-badge badge-ref">Ref</span>
+        </div>
+        <p class="card-desc">Evidence folder layouts, session database tracking, audit trails, and long-term memory approvals flow.</p>
+        <div class="card-footer">
+          <span class="path">evidence-and-memory.md</span>
+          <span class="feature">State Explorer</span>
+        </div>
+      </a>
+      <!-- Card: Skills Marketplace -->
+      <a href="skills_blueprint.html" class="doc-card" data-categories="skills" data-title="Skills Marketplace" data-tags="skills marketplace registry local catalog index publish git hub">
+        <div class="card-top">
+          <h3 class="card-title">Skills Marketplace</h3>
+          <span class="card-badge badge-ref">Ref</span>
+        </div>
+        <p class="card-desc">Skills Hub discovery interface, local catalog and index sources, and publisher checklists.</p>
+        <div class="card-footer">
+          <span class="path">skills-marketplace.md</span>
+          <span class="feature">Marketplace Lab</span>
+        </div>
+      </a>
+      <!-- Card: Model Catalog & Routing -->
+      <a href="models_blueprint.html" class="doc-card" data-categories="models" data-title="Model Catalog &amp; Routing" data-tags="models catalog routing probeCapabilitiesForModel offline fallback details">
+        <div class="card-top">
+          <h3 class="card-title">Model Catalog &amp; Routing</h3>
+          <span class="card-badge badge-ref">Ref</span>
+        </div>
+        <p class="card-desc">Model capability matching, exact-id selector `probeCapabilitiesForModel`, live probes (`--offline` toggle), reasoning configurations, and model routing rules.</p>
+        <div class="card-footer">
+          <span class="path">model-catalog.md</span>
+          <span class="feature">Prober Lab</span>
+        </div>
+      </a>
+      <!-- Card: Evaluation Runner -->
+      <a href="eval_blueprint.html" class="doc-card" data-categories="validation" data-title="Evaluation Runner" data-tags="eval runner validation suites YAML baseline metrics dual tokens receiptUsage">
+        <div class="card-top">
+          <h3 class="card-title">Evaluation Runner</h3>
+          <span class="card-badge badge-ref">Ref</span>
+        </div>
+        <p class="card-desc">YAML eval configuration, dual token accountings (wire `tokens.*` vs journal `receiptUsage.*`), EvalArtifactV4 format, and verify.measure task outcome recording.</p>
+        <div class="card-footer">
+          <span class="path">eval-runner.md</span>
+          <span class="feature">Eval Planner</span>
+        </div>
+      </a>
+      <!-- Card: Scientific Validation -->
+      <a href="validation_blueprint.html" class="doc-card" data-categories="validation" data-title="Scientific Validation" data-tags="scientific validation contract numerical tolerance HPC float">
+        <div class="card-top">
+          <h3 class="card-title">Scientific Validation</h3>
+          <span class="card-badge badge-ref">Ref</span>
+        </div>
+        <p class="card-desc">Floating-point numeric assertions, scientific file format checks, and HPC execution gating.</p>
+        <div class="card-footer">
+          <span class="path">scientific-validation.md</span>
+          <span class="feature">Tolerance Calc</span>
+        </div>
+      </a>
+      <!-- Card: Code Evolution -->
+      <a href="evolution_blueprint.html" class="doc-card" data-categories="validation" data-title="Code Evolution" data-tags="evolution manifests json evolve audit pipeline atomic">
+        <div class="card-top">
+          <h3 class="card-title">Code Evolution</h3>
+          <span class="card-badge badge-ref">Ref</span>
+        </div>
+        <p class="card-desc">Falsifiable change manifest schema, atomic execution sequence, and `clio-coder evolve` command guidelines.</p>
+        <div class="card-footer">
+          <span class="path">evolution.md</span>
+          <span class="feature">Manifest Editor</span>
+        </div>
+      </a>
+      <!-- Card: Middleware & Components -->
+      <a href="middleware_blueprint.html" class="doc-card" data-categories="fleet" data-title="Middleware &amp; Components" data-tags="middleware hooks register effect components snapshots budget">
+        <div class="card-top">
+          <h3 class="card-title">Middleware &amp; Components</h3>
+          <span class="card-badge badge-ref">Ref</span>
+        </div>
+        <p class="card-desc">Subsystem hooks, phase-aware middleware hook budgets (DEFAULT_MIDDLEWARE_HOOK_BUDGETS_MS), effect kinds, and runtime component interfaces.</p>
+        <div class="card-footer">
+          <span class="path">middleware-and-components.md</span>
+          <span class="feature">Hook Flow</span>
+        </div>
+      </a>
+      <!-- Card: Observability -->
+      <a href="observability_blueprint.html" class="doc-card" data-categories="obs" data-title="Observability" data-tags="observability spine receipts view dashboard cost telemetry">
+        <div class="card-top">
+          <h3 class="card-title">Observability</h3>
+          <span class="card-badge badge-ref">Ref</span>
+        </div>
+        <p class="card-desc">Saved tool output viewing, step log audits, and execution cost visual metrics.</p>
+        <div class="card-footer">
+          <span class="path">observability.md</span>
+          <span class="feature">Receipt Checker</span>
+        </div>
+      </a>
+      <!-- Card: Extensions & Sharing -->
+      <a href="extensions_blueprint.html" class="doc-card" data-categories="skills" data-title="Extensions &amp; Sharing" data-tags="extensions packages manifests prompt skills archive sharing">
+        <div class="card-top">
+          <h3 class="card-title">Extensions &amp; Sharing</h3>
+          <span class="card-badge badge-ref">Ref</span>
+        </div>
+        <p class="card-desc">Precedence directories overlays, extensions packaging manifest files, and share format definitions.</p>
+        <div class="card-footer">
+          <span class="path">extensions-and-sharing.md</span>
+          <span class="feature">Manifest Builder</span>
+        </div>
+      </a>
+      <!-- Card: Documentation Guide -->
+      <a href="documentation_blueprint.html" class="doc-card" data-categories="reference" data-title="Documentation Guide" data-tags="documentation guide structure style standards checker lint">
+        <div class="card-top">
+          <h3 class="card-title">Documentation Guide</h3>
+          <span class="card-badge badge-ref">Ref</span>
+        </div>
+        <p class="card-desc">Source-first standards, documentation directory structure, claims classes, and markdown linter script.</p>
+        <div class="card-footer">
+          <span class="path">documentation-guide.md</span>
+          <span class="feature">Claims Linter</span>
+        </div>
+      </a>
+      <!-- Card: TUI Design System -->
+      <a href="tui_design_blueprint.html" class="doc-card" data-categories="operate,internal" data-title="TUI Design System" data-tags="tui UI colors glyphs formatting state choreograph visual contextReserve">
+        <div class="card-top">
+          <h3 class="card-title">TUI Design System</h3>
+          <span class="card-badge badge-internal">Internal</span>
+        </div>
+        <p class="card-desc">Interface layout colors palette, Unicode character vocabulary (contextReserve ▒), terminal state drawing choreographies.</p>
+        <div class="card-footer">
+          <span class="path">tui-design.md</span>
+          <span class="feature">Color Lab</span>
+        </div>
+      </a>
+      <!-- Card: Worker Dispatch Mechanics -->
+      <a href="worker_dispatch_blueprint.html" class="doc-card" data-categories="fleet,internal" data-title="Worker Dispatch Mechanics" data-tags="worker processes environment NDJSON protocol heartbeats exit attestation">
+        <div class="card-top">
+          <h3 class="card-title">Worker Dispatch Mechanics</h3>
+          <span class="card-badge badge-internal">Internal</span>
+        </div>
+        <p class="card-desc">NDJSON parent-child socket stream protocols, 13-field worker attestation frame, timeout watchdog timing, and exit status mapping.</p>
+        <div class="card-footer">
+          <span class="path">worker-dispatch-mechanics.md</span>
+          <span class="feature">Protocol Sim</span>
+        </div>
+      </a>
+      <!-- Card: Internal Eval Suites -->
+      <a href="evals_internal_blueprint.html" class="doc-card" data-categories="validation,internal" data-title="Internal Eval Suites" data-tags="evals internal seeds regression prompt matrices gates">
+        <div class="card-top">
+          <h3 class="card-title">Internal Eval Suites</h3>
+          <span class="card-badge badge-internal">Internal</span>
+        </div>
+        <p class="card-desc">Regression test directories, prompt validation matrices, and internal model quality gates.</p>
+        <div class="card-footer">
+          <span class="path">evals-internal.md</span>
+          <span class="feature">Gates Check</span>
+        </div>
+      </a>
+      <!-- Card: Config Knobs Audit -->
+      <a href="config_knobs_audit_blueprint.html" class="doc-card" data-categories="configure,internal" data-title="Config Knobs Audit" data-tags="audit historical legacy knobs vars settings cleanup">
+        <div class="card-top">
+          <h3 class="card-title">Config Knobs Audit</h3>
+          <span class="card-badge badge-internal">Historical</span>
+        </div>
+        <p class="card-desc">Audit documentation tracking consolidated environment variables, old settings layout, and design findings.</p>
+        <div class="card-footer">
+          <span class="path">config-knobs-audit.md</span>
+          <span class="feature">Knobs Auditor</span>
+        </div>
+      </a>
+      <!-- Card: Session Lifecycle -->
+      <a href="../session-lifecycle.md" class="doc-card" data-categories="operate,reference" data-title="Session Lifecycle" data-tags="session ledger tree jsonl fork resume checkpoint active path migrations">
+        <div class="card-top">
+          <h3 class="card-title">Session Lifecycle</h3>
+          <span class="card-badge badge-markdown">Markdown Spec</span>
+        </div>
+        <p class="card-desc">Session ledger v3, conversation tree graph, active-path lineage selection, /fork, /resume, checkpoints, and write-ahead protected artifact journal.</p>
+        <div class="card-footer">
+          <span class="path">session-lifecycle.md</span>
+          <span class="feature" style="color: #a5b4fc;">Ledger Format v3 ↗</span>
+        </div>
+      </a>
+      <!-- Card: ACP Server -->
+      <a href="../acp.md" class="doc-card" data-categories="operate,reference" data-title="ACP Protocol Server" data-tags="acp agent client protocol jsonrpc stdio permissions mediator zed errors">
+        <div class="card-top">
+          <h3 class="card-title">ACP Protocol Server</h3>
+          <span class="card-badge badge-markdown">Markdown Spec</span>
+        </div>
+        <p class="card-desc">Agent Client Protocol (ACP v1 / schema 0.4.5) JSON-RPC server over stdio, tool mediation, non-stall permission handling, and error taxonomy.</p>
+        <div class="card-footer">
+          <span class="path">acp.md</span>
+          <span class="feature" style="color: #a5b4fc;">JSON-RPC 2.0 ↗</span>
+        </div>
+      </a>
+      <!-- Card: Artifact Versions -->
+      <a href="../artifact-versions.md" class="doc-card" data-categories="reference" data-title="Artifact Versions" data-tags="versions receipt integrity session format workerspec fleet eval trace schema migration">
+        <div class="card-top">
+          <h3 class="card-title">Artifact Versions</h3>
+          <span class="card-badge badge-markdown">Markdown Spec</span>
+        </div>
+        <p class="card-desc">Authoritative registry and migration policies for all 9 serialized artifact schemas across Clio Coder.</p>
+        <div class="card-footer">
+          <span class="path">artifact-versions.md</span>
+          <span class="feature" style="color: #a5b4fc;">Version Registry ↗</span>
+        </div>
+      </a>
+      <!-- Card: Exit Codes & Output Contracts -->
+      <a href="../exit-codes-and-output.md" class="doc-card" data-categories="operate,reference" data-title="Exit Codes &amp; Output Contracts" data-tags="exit codes status help json streaming stdout stderr format cli">
+        <div class="card-top">
+          <h3 class="card-title">Exit Codes &amp; Output</h3>
+          <span class="card-badge badge-markdown">Markdown Spec</span>
+        </div>
+        <p class="card-desc">Deterministic process exit code taxonomy (0, 1, 2, 3), --help standard on stdout, and machine-readable JSON streaming contracts.</p>
+        <div class="card-footer">
+          <span class="path">exit-codes-and-output.md</span>
+          <span class="feature" style="color: #a5b4fc;">Exit Taxonomy ↗</span>
+        </div>
+      </a>
+      <!-- Card: Capacity Leases & Scheduling -->
+      <a href="../capacity-and-scheduling.md" class="doc-card" data-categories="fleet,reference" data-title="Capacity Leases &amp; Scheduling" data-tags="capacity leases scheduling drain lock ttl admission cluster dispatch">
+        <div class="card-top">
+          <h3 class="card-title">Capacity &amp; Scheduling</h3>
+          <span class="card-badge badge-markdown">Markdown Spec</span>
+        </div>
+        <p class="card-desc">Multi-process capacity leasing (dispatch-admission.json), heartbeat TTLs, cross-process transaction locks, and cluster drain control.</p>
+        <div class="card-footer">
+          <span class="path">capacity-and-scheduling.md</span>
+          <span class="feature" style="color: #a5b4fc;">Leasing Protocol ↗</span>
+        </div>
+      </a>
+      <!-- Card: Glossary -->
+      <a href="../glossary.md" class="doc-card" data-categories="reference" data-title="Glossary" data-tags="glossary terms assignment run attempt batch plan receipt topology types">
+        <div class="card-top">
+          <h3 class="card-title">Glossary</h3>
+          <span class="card-badge badge-markdown">Markdown Spec</span>
+        </div>
+        <p class="card-desc">Authoritative definitions of 17 core architectural concepts mapped to their owning TypeScript types in src/.</p>
+        <div class="card-footer">
+          <span class="path">glossary.md</span>
+          <span class="feature" style="color: #a5b4fc;">17 Core Terms ↗</span>
+        </div>
+      </a>
+      <!-- Card: Troubleshooting -->
+      <a href="../troubleshooting.md" class="doc-card" data-categories="operate,reference" data-title="Troubleshooting" data-tags="troubleshooting errors remedies diagnostics doctor probe repair warnings">
+        <div class="card-top">
+          <h3 class="card-title">Troubleshooting</h3>
+          <span class="card-badge badge-markdown">Markdown Spec</span>
+        </div>
+        <p class="card-desc">Actionable error remediation and diagnostics catalog keyed by exact user-facing messages and failure codes.</p>
+        <div class="card-footer">
+          <span class="path">troubleshooting.md</span>
+          <span class="feature" style="color: #a5b4fc;">Error Matrix ↗</span>
+        </div>
+      </a>
+    </main>
+    <!-- Quick Start Section -->
+    <div class="glass-card" style="margin-top: 3.5rem;">
+      <h3 style="font-size: 1.25rem; font-weight: 700; color: #ffffff; margin-bottom: 1rem; display: flex; align-items: center; gap: 0.5rem;">
+        <svg width="18" height="18" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><title>Icon</title><polygon points="5 3 19 12 5 21 5 3"></polygon></svg>
+        CLI Quick Reference
+      </h3>
+      <p style="margin-bottom: 1rem; color: var(--text-muted);">Launch the visual docs server from your local Clio checkout workspace environment:</p>
+      <pre><code># Start local http server and open landing page
+clio-coder docs
+# Jump directly to safety specs page
+clio-coder docs safety
+# Print only the bound port url without launching a browser
+clio-coder docs --no-open</code></pre>
+    </div>
+    <footer>
+      <p>Clio Coder Visual Documentation Center &bull; Version 0.3.0</p>
+      <p>Maintainer: Illinois Institute of Technology / Gnosis Research Center &bull; iowarp.ai</p>
+    </footer>
+  </div>
+  <script>
+    let activeCategory = 'all';
+    function setCategory(catId) {
+      activeCategory = catId;
+      // Update buttons
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+    function filterCards() {
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+        const title = card.getAttribute('data-title').toLowerCase();
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