genoma-evolution 1.0.0

package/.claude/worktrees/phase-2-mcp/.brv/context-tree/frontend/src/settingspage.md

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+---
+title: SettingsPage
+summary: ''
+tags: []
+related: []
+keywords: []
+createdAt: '2026-04-28T01:33:30.556Z'
+updatedAt: '2026-04-28T01:33:30.556Z'
+---
+## Reason
+Preserving complete src/components/pages/SettingsPage.tsx from hermes-dashboard project
+
+## Raw Concept
+**Task:**
+Preserve src/components/pages/SettingsPage.tsx
+
+**Files:**
+- src/components/pages/SettingsPage.tsx
+
+**Timestamp:** 2026-04-28
+
+**Patterns:**
+- `SettingsPage` - Component or function
+
+## Narrative
+### Structure
+TSX file with 1 components/functions
+
+### Highlights
+Source: hermes-dashboard/src/components/pages/SettingsPage.tsx
+
+---
+
+
+"use client";
+
+import { useState, useEffect } from "react";
+import { motion } from "framer-motion";
+import {
+  Settings,
+  Key,
+  Eye,
+  EyeOff,
+  Check,
+  X,
+  Server,
+  FolderOpen,
+} from "lucide-react";
+import { fetchHealth } from "@/lib/api";
+
+interface EnvVar {
+  key: string;
+  value: string;
+  desc: string;
+}
+
+export default function SettingsPage() {
+  const [health, setHealth] = useState<{
+    status: string;
+    hermes_repo: string;
+    hermes_repo_exists: boolean;
+    evolution_dir: string;
+    evolution_dir_exists: boolean;
+    skills_count: number;
+  } | null>(null);
+
+  const [showKeys, setShowKeys] = useState<Record<string, boolean>>({});
+
+  useEffect(() => {
+    fetchHealth().then(setHealth).catch(() => {});
+  }, []);
+
+  const envVars: EnvVar[] = [
+    { key: "OPENAI_API_KEY", value: "sk-...", desc: "Used by DSPy for LLM calls" },
+    { key: "OPENAI_BASE_URL", value: "http://localhost:11434/v1", desc: "Ollama endpoint" },
+    { key: "HERMES_AGENT_REPO", value: health?.hermes_repo || "~/.hermes/hermes-agent", desc: "Path to hermes-agent repo" },
+  ];
+
+  return (
+    <div className="space-y-6 max-w-3xl">
+      {/* System Paths */}
+      <motion.div initial={{ opacity: 0, y: 15 }} animate={{ opacity: 1, y: 0 }} className="glass-card rounded-2xl p-6">
+        <h2 className="text-sm font-semibold uppercase tracking-wider flex items-center gap-2 mb-4"><Server className="w-4 h-4 text-accent-cyan" />System Paths</h2>
+        {health && (
+          <div className="space-y-3">
+            {[
+              { label: "Hermes Agent Repo", path: health.hermes_repo, exists: health.hermes_repo_exists },
+              { label: "Evolution Engine", path: health.evolution_dir, exists: health.evolution_dir_exists },
+            ].map((item) => (
+              <div key={item.label} className="flex items-center justify-between p-3 rounded-xl bg-white/[0.02] border border-white/[0.04]">
+                <div className="flex items-center gap-3"><FolderOpen className="w-4 h-4 text-muted-foreground" /><div><p className="text-sm font-medium">{item.label}</p><p className="text-[10px] font-mono text-muted-foreground">{item.path}</p></div></div>
+                {item.exists ? <Check className="w-4 h-4 text-success" /> : <X className="w-4 h-4 text-error" />}
+              </div>
+            ))}
+            <div className="flex items-center justify-between p-3 rounded-xl bg-white/[0.02] border border-white/[0.04]">
+              <div className="flex items-center gap-3"><FolderOpen className="w-4 h-4 text-muted-foreground" /><div><p className="text-sm font-medium">Skills Found</p></div></div>
+              <span className="text-sm font-mono text-accent-violet">{health.skills_count}</span>
+            </div>
+          </div>
+        )}
+      </motion.div>
+
+      {/* Environment Variables */}
+      <motion.div initial={{ opacity: 0, y: 15 }} animate={{ opacity: 1, y: 0 }} transition={{ delay: 0.1 }} className="glass-card rounded-2xl p-6">
+        <h2 className="text-sm font-semibold uppercase tracking-wider flex items-center gap-2 mb-4"><Key className="w-4 h-4 text-accent-violet" />Environment Variables</h2>
+        <div className="space-y-3">
+          {envVars.map((env) => (
+            <div key={env.key} className="p-3 rounded-xl bg-white/[0.02] border border-white/[0.04]">
+              <div className="flex items-center justify-between mb-1">
+                <span className="text-xs font-mono text-accent-cyan">{env.key}</span>
+                <button onClick={() => setShowKeys((prev) => ({ ...prev, [env.key]: !prev[env.key] }))} className="text-muted-foreground/50 hover:text-muted-foreground">{showKeys[env.key] ? <EyeOff className="w-3 h-3" /> : <Eye className="w-3 h-3" />}</button>
+              </div>
+              <p className="text-xs font-mono text-muted-foreground">{showKeys[env.key] ? env.value : "••••••••••••"}</p>
+              <p className="text-[10px] text-muted-foreground/50 mt-1">{env.desc}</p>
+            </div>
+          ))}
+        </div>
+        <p className="text-[10px] text-muted-foreground/40 mt-4">Set these in your shell or .env file. The backend reads them on startup.</p>
+      </motion.div>
+    </div>
+  );
+}
+
+    

package/.claude/worktrees/phase-2-mcp/.brv/context-tree/frontend/src/settingspage.overview.md

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+# SettingsPage Component Overview
+
+**Source:** `src/components/pages/SettingsPage.tsx` from `hermes-dashboard`
+
+## Key Points
+
+- **Client-side React component** (`"use client"`) using `useState`, `useEffect`, and Framer Motion for animations
+- **Fetches health status** from `/lib/api` on mount to display system state
+- **Two main sections:** System Paths and Environment Variables
+- **Toggle visibility** for sensitive values (API keys) with eye/eye-off icons
+- **Visual validation indicators** (Check/X icons) for path existence checks
+- **Hardcoded env var list:** OPENAI_API_KEY, OPENAI_BASE_URL, HERMES_AGENT_REPO
+- **Styling:** Uses glass-card class, Tailwind-like classes, Lucide React icons
+
+## Structure / Sections
+
+1. **System Paths** — Displays Hermes Agent Repo, Evolution Engine paths with existence checks; shows skills count
+2. **Environment Variables** — Lists sensitive config (API keys, endpoints) with show/hide toggle functionality
+
+## Notable Entities & Patterns
+
+| Entity | Purpose |
+|--------|---------|
+| `EnvVar` interface | `{ key, value, desc }` shape for env display |
+| `fetchHealth()` | API call to get system status from `@/lib/api` |
+| `showKeys` state | Record toggle for masking/unmasking values |
+| Health object | `{ status, hermes_repo, hermes_repo_exists, evolution_dir, evolution_dir_exists, skills_count }` |
+
+## Decisions
+
+- Health data is fetched silently (empty catch block) — no user feedback on failure
+- Env vars are hardcoded/static list, not dynamically loaded from backend
+- Keys masked by default as `"••••••••••••"` placeholder
+- Path existence shown with green checkmark or red X icons

package/.claude/worktrees/phase-2-mcp/.brv/context-tree/frontend/src/sidebar.md

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+---
+title: Sidebar
+summary: ''
+tags: []
+related: []
+keywords: []
+createdAt: '2026-04-28T01:33:30.557Z'
+updatedAt: '2026-04-28T01:33:30.557Z'
+---
+## Reason
+Preserving complete src/components/Sidebar.tsx from hermes-dashboard project
+
+## Raw Concept
+**Task:**
+Preserve src/components/Sidebar.tsx
+
+**Files:**
+- src/components/Sidebar.tsx
+
+**Timestamp:** 2026-04-28
+
+**Patterns:**
+- `Sidebar` - Component or function
+
+## Narrative
+### Structure
+TSX file with 1 components/functions
+
+### Highlights
+Source: hermes-dashboard/src/components/Sidebar.tsx
+
+---
+
+
+"use client";
+
+import { useState } from "react";
+import { motion, AnimatePresence } from "framer-motion";
+import {
+  Layers,
+  GitBranch,
+  Database,
+  Brain,
+  BarChart3,
+  Terminal as TerminalIcon,
+  Settings,
+  Dna,
+  ChevronLeft,
+  ChevronRight,
+  Cpu,
+  BookOpen,
+  Bot,
+  Sparkles,
+} from "lucide-react";
+
+export type Page =
+  | "overview"
+  | "skills"
+  | "evolution"
+  | "datasets"
+  | "memory"
+  | "metrics"
+  | "logs"
+  | "settings"
+;
+
+interface NavItem {
+  id: Page;
+  label: string;
+  icon: React.ReactNode;
+}
+
+const navItems: NavItem[] = [
+  { id: "overview", label: "Overview", icon: <Layers className="w-4 h-4" /> },
+  { id: "skills", label: "Skill Hub", icon: <Sparkles className="w-4 h-4" /> },
+  { id: "evolution", label: "Evolution", icon: <GitBranch className="w-4 h-4" /> },
+  { id: "datasets", label: "Datasets", icon: <Database className="w-4 h-4" /> },
+  { id: "memory", label: "Memory", icon: <Brain className="w-4 h-4" /> },
+  { id: "metrics", label: "Metrics", icon: <BarChart3 className="w-4 h-4" /> },
+  { id: "logs", label: "Live Logs", icon: <TerminalIcon className="w-4 h-4" /> },
+  { id: "settings", label: "Settings", icon: <Settings className="w-4 h-4" /> },
+];
+
+interface SidebarProps {
+  activePage: Page;
+  onNavigate: (page: Page) => void;
+}
+
+export default function Sidebar({ activePage, onNavigate }: SidebarProps) {
+  const [collapsed, setCollapsed] = useState(false);
+
+  return (
+    <motion.aside
+      animate={{ width: collapsed ? 64 : 240 }}
+      transition={{ duration: 0.2, ease: "easeOut" }}
+      className="h-screen sticky top-0 flex flex-col border-r border-[#B2FFFF]/20 bg-[#E8F9FA] dark:bg-[#061014] backdrop-blur-xl transition-colors duration-300"
+    >
+      {/* Logo */}
+      <div className="flex items-center gap-3 px-4 h-16 border-b border-[#B2FFFF]/15 dark:border-white/[0.06]">
+        <div className="w-8 h-8 rounded-lg bg-[#0891B2] dark:bg-[#06B6D4] flex items-center justify-center flex-shrink-0 shadow-sm shadow-[#0891B2]/20">
+          <Dna className="w-4 h-4 text-white" />
+        </div>
+        <AnimatePresence>
+          {!collapsed && (
+            <motion.div
+              initial={{ opacity: 0, x: -10 }}
+              animate={{ opacity: 1, x: 0 }}
+              exit={{ opacity: 0, x: -10 }}
+              className="overflow-hidden"
+            >
+              <span className="text-sm font-semibold tracking-tight text-[#0F172A] dark:text-white">Hermes</span>
+              <p className="text-[10px] text-[#475569] dark:text-slate-400">Evolution Dashboard</p>
+            </motion.div>
+          )}
+        </AnimatePresence>
+      </div>
+
+      {/* Nav items */}
+      <nav className="flex-1 py-4 px-2 space-y-1 overflow-y-auto">
+        {navItems.map((item) => (
+          <button
+            key={item.id}
+            onClick={() => onNavigate(item.id)}
+            className={`w-full flex items-center gap-3 px-3 py-2.5 rounded-xl text-sm transition-all duration-200 ${
+              activePage === item.id
+                ? "bg-[#B2FFFF]/40 text-[#0E7490] dark:bg-[#B2FFFF]/20 dark:text-[#E0FFFF] shadow-sm shadow-[#B2FFFF]/10"
+                : "text-[#475569] hover:text-[#0F172A] hover:bg-[#B2FFFF]/20 dark:text-[#B2FFFF] dark:hover:text-[#E0FFFF] dark:hover:bg-[#B2FFFF]/10"
+            }`}
+          >
+            <span
+              className={`flex-shrink-0 ${
+                activePage === item.id ? "text-[#0891B2] dark:text-[#67E8F9]" : ""
+              }`}
+            >
+              {item.icon}
+            </span>
+            <AnimatePresence>
+              {!collapsed && (
+                <motion.span
+                  initial={{ opacity: 0 }}
+                  animate={{ opacity: 1 }}
+                  exit={{ opacity: 0 }}
+                  className="truncate font-medium"
+                >
+                  {item.label}
+                </motion.span>
+              )}
+            </AnimatePresence>
+          </button>
+        ))}
+      </nav>
+
+      {/* Collapse toggle */}
+      <div className="p-2 border-t border-[#B2FFFF]/15 dark:border-[#B2FFFF]/10">
+        <button
+          onClick={() => setCollapsed(!collapsed)}
+          className="w-full flex items-center justify-center p-2 rounded-xl text-[#475569] hover:text-[#0F172A] hover:bg-[#B2FFFF]/20 dark:text-[#A5F3FC]/70 dark:hover:text-[#E0FFFF] dark:hover:bg-[#B2FFFF]/10 transition-colors"
+        >
+          {collapsed ? (
+            <ChevronRight className="w-4 h-4" />
+          ) : (
+            <ChevronLeft className="w-4 h-4" />
+          )}
+        </button>
+      </div>
+    </motion.aside>
+  );
+}
+
+    

package/.claude/worktrees/phase-2-mcp/.brv/context-tree/frontend/src/sidebar.overview.md

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+## Key Points
+
+- **Sidebar component** from `hermes-dashboard` project - a collapsible navigation sidebar with animated transitions
+- **Navigation structure** supports 8 pages: Overview, Skill Hub, Evolution, Datasets, Memory, Metrics, Live Logs, and Settings
+- **Built with React + TypeScript**, using `framer-motion` for smooth expand/collapse animations and `lucide-react` for icons
+- **Features collapse toggle** that animates width from 240px to 64px with a 0.2s easeOut transition
+- **Dark mode support** via CSS custom properties (`dark:bg-[#061014]`, `dark:text-[#E0FFFF]`)
+- **Active page highlighting** with cyan tint backgrounds and shadow effects
+- **Uses `"use client"`** directive, indicating this is a client-side component in a Next.js app
+
+## Structure / Sections Summary
+
+1. **Type Definitions**
+   - `Page` union type for 8 distinct routes
+   - `NavItem` interface with `id`, `label`, and `icon` properties
+
+2. **Navigation Data**
+   - `navItems` array mapping each page to a label and lucide icon
+
+3. **Component Props**
+   - `SidebarProps` interface accepting `activePage` and `onNavigate` callback
+
+4. **Main Component**
+   - `Sidebar` function with local `collapsed` state
+   - Renders animated

package/.claude/worktrees/phase-2-mcp/.brv/context-tree/meta/_index.md

@@ -0,0 +1,24 @@
+---
+children_hash: dc15e2143853c4d58bd92cf78377d8722d8f607d734e4df57815b80539e86ae2
+compression_ratio: 0.6743119266055045
+condensation_order: 2
+covers: [curation_context/_index.md]
+covers_token_total: 218
+summary_level: d2
+token_count: 147
+type: summary
+---
+# Meta Domain
+
+## Overview
+
+The Meta domain contains knowledge about the curation system itself—its workflows, attempts, and operational patterns.
+
+## Child Entry Summary
+
+- **curation_context** — Documents curation workflow outcomes, including unsuccessful attempts where input variables contained only placeholder characters with no extractable facts. Serves as operational metadata for distinguishing processed content from empty inputs.
+
+## Key Relationships
+
+- Curation context tracks workflow patterns at `meta/curation_context/`
+- Provides audit trail for curation session outcomes

package/.claude/worktrees/phase-2-mcp/.brv/context-tree/meta/curation_context/_index.md

@@ -0,0 +1,24 @@
+---
+children_hash: ce72a395bf10a82836c973904202f721c5fbcdd57b8e612e44466deac2c68fd8
+compression_ratio: 0.7358490566037735
+condensation_order: 1
+covers: [empty_context.md]
+covers_token_total: 212
+summary_level: d1
+token_count: 156
+type: summary
+---
+# Meta: Curation Context
+
+## Overview
+
+This domain records context curation attempts from RLM sessions where input variables were empty or contained no actionable content.
+
+## Key Pattern
+
+- **empty_context.md** — Documents instances where the context variable contained only placeholder characters (e.g., ".") with no extractable facts. Serves as a record of unsuccessful curation attempts to distinguish from genuinely processed content.
+
+## Relationships
+
+- child entries reference abstract and overview variants at `meta/curation_context/`
+- Used to track curation workflow outcomes and prevent reprocessing empty inputs

package/.claude/worktrees/phase-2-mcp/.brv/context-tree/meta/curation_context/empty_context.abstract.md

@@ -0,0 +1,4 @@
+---
+related: [meta/curation_context/empty_context.md, meta/curation_context/empty_context.overview.md]
+---
+The context variable contained only a dot, resulting in no facts being extracted.

package/.claude/worktrees/phase-2-mcp/.brv/context-tree/meta/curation_context/empty_context.md

@@ -0,0 +1,35 @@
+---
+createdAt: '2026-04-23T05:47:41.687Z'
+keywords: []
+related: [meta/curation_context/empty_context.abstract.md, meta/curation_context/empty_context.overview.md]
+summary: Context variable was empty (single dot), no facts extracted
+tags: []
+title: Empty Context
+updatedAt: '2026-04-23T05:47:41.687Z'
+---
+## Reason
+Documenting that the context variable contained only a dot with no meaningful content
+
+## Raw Concept
+**Task:**
+Curate empty context from RLM session
+
+**Changes:**
+- Context variable contained only a dot
+
+**Flow:**
+Received context -> recon -> determined single-pass -> no facts -> curated meta context
+
+**Timestamp:** 2026-04-23
+
+**Author:** Context Engineer
+
+## Narrative
+### Structure
+No actual content to curate; context variable was "."
+
+### Dependencies
+None
+
+### Highlights
+No facts extracted due to lack of meaningful input

package/.claude/worktrees/phase-2-mcp/.brv/context-tree/meta/curation_context/empty_context.overview.md

@@ -0,0 +1,20 @@
+---
+related: [meta/curation_context/empty_context.md, meta/curation_context/empty_context.abstract.md]
+---
+**Key Points**
+- The context variable contained only a single dot (".") with no meaningful content.  
+- No facts were extracted because the input lacked substantive information.  
+- The document records the reasoning and workflow for handling an empty context in an RLM session.  
+- A "meta context" was curated to document the absence of data.  
+- The entry was created and updated on 2026-04-23 by the Context Engineer.  
+
+**Structure / Sections Summary**
+- **Front‑matter**: title, summary, tags, related, keywords, timestamps.  
+- **Reason**: brief statement explaining why the document exists (empty context).  
+- **Raw Concept**: details the task, changes observed, flow of processing, timestamp, and author.  
+- **Narrative**: describes the structure (no content), dependencies (none), and highlights (no facts extracted).  
+
+**Notable Entities, Patterns, or Decisions**
+- **Entities**: Context Engineer, RLM session, context variable, meta context.  
+- **Patterns**: Detection of a single‑dot context → single‑pass determination → zero fact extraction → creation of a meta‑context record.  
+- **Decisions**: Determined that the context required only a single pass; concluded no facts could be extracted; opted to curate an empty‑context meta record for traceability.

package/.claude/worktrees/phase-2-mcp/.brv/dream-log/drm-1777341062653.json

@@ -0,0 +1,33 @@
+{
+  "completedAt": 1777341186404,
+  "id": "drm-1777341062653",
+  "operations": [
+    {
+      "action": "CROSS_REFERENCE",
+      "inputFiles": [
+        "meta/curation_context/empty_context.md",
+        "meta/curation_context/empty_context.abstract.md",
+        "meta/curation_context/empty_context.overview.md"
+      ],
+      "needsReview": false,
+      "previousTexts": {
+        "meta/curation_context/empty_context.md": "---\ntitle: Empty Context\nsummary: Context variable was empty (single dot), no facts extracted\ntags: []\nrelated: []\nkeywords: []\ncreatedAt: '2026-04-23T05:47:41.687Z'\nupdatedAt: '2026-04-23T05:47:41.687Z'\n---\n## Reason\nDocumenting that the context variable contained only a dot with no meaningful content\n\n## Raw Concept\n**Task:**\nCurate empty context from RLM session\n\n**Changes:**\n- Context variable contained only a dot\n\n**Flow:**\nReceived context -> recon -> determined single-pass -> no facts -> curated meta context\n\n**Timestamp:** 2026-04-23\n\n**Author:** Context Engineer\n\n## Narrative\n### Structure\nNo actual content to curate; context variable was \".\"\n\n### Dependencies\nNone\n\n### Highlights\nNo facts extracted due to lack of meaningful input\n",
+        "meta/curation_context/empty_context.abstract.md": "The context variable contained only a dot, resulting in no facts being extracted.",
+        "meta/curation_context/empty_context.overview.md": "**Key Points**\n- The context variable contained only a single dot (\".\") with no meaningful content.  \n- No facts were extracted because the input lacked substantive information.  \n- The document records the reasoning and workflow for handling an empty context in an RLM session.  \n- A \"meta context\" was curated to document the absence of data.  \n- The entry was created and updated on 2026-04-23 by the Context Engineer.  \n\n**Structure / Sections Summary**\n- **Front‑matter**: title, summary, tags, related, keywords, timestamps.  \n- **Reason**: brief statement explaining why the document exists (empty context).  \n- **Raw Concept**: details the task, changes observed, flow of processing, timestamp, and author.  \n- **Narrative**: describes the structure (no content), dependencies (none), and highlights (no facts extracted).  \n\n**Notable Entities, Patterns, or Decisions**\n- **Entities**: Context Engineer, RLM session, context variable, meta context.  \n- **Patterns**: Detection of a single‑dot context → single‑pass determination → zero fact extraction → creation of a meta‑context record.  \n- **Decisions**: Determined that the context required only a single pass; concluded no facts could be extracted; opted to curate an empty‑context meta record for traceability."
+      },
+      "reason": "These are complementary context tree companion files for the 'Empty Context' entry: the main .md contains full content with rawConcept and narrative, the .abstract.md provides a one-sentence summary, and the .overview.md provides a structured breakdown with key points. They serve distinct purposes in the context tree hierarchy and should remain separate with frontmatter cross-references linking them.",
+      "type": "CONSOLIDATE"
+    }
+  ],
+  "startedAt": 1777341062653,
+  "status": "completed",
+  "summary": {
+    "consolidated": 1,
+    "errors": 0,
+    "flaggedForReview": 0,
+    "pruned": 0,
+    "synthesized": 0
+  },
+  "taskId": "fad4a202-0e75-4157-91fd-7ddc01d84c85",
+  "trigger": "agent-idle"
+}

package/.claude/worktrees/phase-2-mcp/.brv/dream-state.json

@@ -0,0 +1,8 @@
+{
+  "curationsSinceDream": 1,
+  "lastDreamAt": "2026-04-28T01:53:06.404Z",
+  "lastDreamLogId": "drm-1777341062653",
+  "pendingMerges": [],
+  "totalDreams": 1,
+  "version": 1
+}