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+# Gemini CLI Bot (Cognitive Repository)
+
+This directory contains the foundational architecture for the `gemini-cli-bot`,
+transforming the repository into a proactive, evolutionary system.
+
+It implements a dual-layer approach to balance immediate responsiveness with
+long-term strategic optimization.
+
+## Layered Execution Model
+
+### 1. System 1: The Pulse (Reflex Layer)
+
+- **Purpose**: High-frequency, deterministic maintenance.
+- **Frequency**: 30-minute cron (`.github/workflows/gemini-cli-bot-pulse.yml`).
+- **Implementation**: Pure TypeScript/JavaScript scripts.
+- **Classification**: Optionally utilizes Gemini CLI for high-confidence
+  semantic classification (e.g., triage, labeling, sentiment) while preferring
+  deterministic logic for equivalent tasks.
+- **Phases**:
+  - **Reflex Execution**: Runs triage, routing, and automated maintenance
+    scripts in `reflexes/scripts/`.
+- **Output**: Real-time action execution.
+
+### 2. System 2: The Brain (Reasoning Layer)
+
+- **Purpose**: Strategic investigation, policy refinement, and proactive
+  self-optimization.
+- **Frequency**: 24-hour cron (`.github/workflows/gemini-cli-bot-brain.yml`).
+- **Implementation**: Agentic Gemini CLI phases.
+- **Phases**:
+  - **Metrics Collection**: Executes scripts in `metrics/scripts/` to track
+    repository health (Open issues, PR latency, throughput, etc.).
+  - **Phase 1: Reasoning (Metrics & Root-Cause Analysis)**: Analyzes time-series
+    metric trends and repository state to identify bottlenecks or productivity
+    gaps, tests hypotheses, and proposes script or configuration changes to
+    improve repository health and maintainability.
+  - **Phase 2: Critique**: A technical and logical validation layer that reviews
+    proposed changes for robustness, actor-awareness, and anti-spam protocols.
+  - **Phase 3: Publish**: Automatically promotes approved changes to Pull
+    Requests, handles branch management, and responds to maintainer feedback.
+
+## Directory Structure
+
+- `metrics/`: Deterministic runner (`index.ts`) and scripts for tracking
+  repository metrics via GitHub CLI.
+- `reflexes/scripts/`: Deterministic triage and routing scripts executed by the
+  Pulse.
+- `brain/`: Prompt templates and logic for strategic root-cause analysis (Phase
+  1: `metrics.md`) and technical validation (Phase 2: `critique.md`).
+- `history/`: Persistent storage for time-series metrics artifacts.
+- `lessons-learned.md`: The bot's structured memory, containing the Task Ledger,
+  Hypothesis Ledger, and Decision Log.
+
+## Usage
+
+### Local Metrics Collection
+
+To manually collect repository metrics locally, run the following command from
+the workspace root:
+
+```bash
+npx tsx tools/gemini-cli-bot/metrics/index.ts
+```
+
+This will execute all scripts within `metrics/scripts/` and output the results
+to `tools/gemini-cli-bot/history/metrics-before.csv`.
+
+### Development
+
+When modifying the bot's logic:
+
+1. **Reflexes**: Add or update scripts in `reflexes/scripts/`.
+2. **Reasoning**: Update the prompts in `brain/` to refine how the bot
+   identifies bottlenecks.
+3. **Critique**: Update the prompts in `critique/` to strengthen the validation
+   of proposed changes.