Update file permissions and add documentation for LLM integration

cline_docs/systemPatterns.md

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+# System Patterns
+Last Updated: 2024-12-27
+
+## High-level Architecture
+
+### Current System
+```
+Discord Events -> Message Processing -> SQLite Storage
+                                   -> Markov Generation
+```
+
+### Proposed LLM Integration
+```
+Discord Events -> Message Processing -> SQLite Storage
+                                   -> Response Generator
+                                      ├─ Markov Chain
+                                      ├─ LLM
+                                      └─ Response Selector
+```
+
+## Core Technical Patterns
+
+### Data Storage
+- SQLite database using TypeORM
+- Entity structure:
+  - Guild (server)
+  - Channel (per-server channels)
+  - Messages (training data)
+
+### Message Processing
+1. Current Flow:
+   - Message received
+   - Filtered for human authorship
+   - Stored in database with metadata
+   - Used for Markov chain training
+
+2. Enhanced Flow:
+   - Add message embedding generation
+   - Store context window
+   - Track conversation threads
+
+### Response Generation
+
+#### Current (Markov)
+```typescript
+interface MarkovGenerateOptions {
+  filter: (result) => boolean;
+  maxTries: number;
+  startSeed?: string;
+}
+```
+
+#### Proposed (Hybrid)
+```typescript
+interface ResponseGenerateOptions {
+  contextWindow: Message[];
+  temperature: number;
+  maxTokens: number;
+  startSeed?: string;
+  forceProvider?: 'markov' | 'llm' | 'hybrid';
+}
+```
+
+## Data Flow
+
+### Training Pipeline
+1. Message Collection
+   - Discord channel history
+   - JSON imports
+   - Real-time messages
+
+2. Processing
+   - Text cleaning
+   - Metadata extraction
+   - Embedding generation
+
+3. Storage
+   - Raw messages
+   - Processed embeddings
+   - Context relationships
+
+### Response Pipeline
+1. Context Gathering
+   - Recent messages
+   - Channel history
+   - User interaction history
+
+2. Generation Strategy
+   - Short responses: Markov chain
+   - Complex responses: LLM
+   - Hybrid: LLM-guided Markov chain
+
+3. Post-processing
+   - Response filtering
+   - Token limit enforcement
+   - Attachment handling
+
+## Key Technical Decisions
+
+### LLM Integration
+1. Local Embedding Model
+   - Use sentence-transformers for message embedding
+   - Store embeddings in SQLite
+   - Enable semantic search
+
+2. Response Generation
+   - Primary: Use OpenAI API
+   - Fallback: Use local LLM
+   - Hybrid: Combine with Markov output
+
+3. Context Management
+   - Rolling window of recent messages
+   - Semantic clustering of related content
+   - Thread-aware context tracking
+
+### Performance Requirements
+1. Response Time
+   - Markov: < 100ms
+   - LLM: < 2000ms
+   - Hybrid: < 2500ms
+
+2. Memory Usage
+   - Max 1GB per guild
+   - Batch processing for large imports
+   - Regular cleanup of old contexts
+
+3. Rate Limiting
+   - Discord API compliance
+   - LLM API quota management
+   - Fallback mechanisms