commit 6a55b32ed97163ad985ecd0558b704ac8e8fd8a3
Author: Shawn Anderson <shawn@longtailfinancial.com>
Date:   Sun Apr 13 09:28:28 2025 -0700

    Publishing initial version of seed script for cognitive ecosystem.

diff --git a/init.fish b/init.fish
new file mode 100755
index 0000000..e631e91
--- /dev/null
+++ b/init.fish
@@ -0,0 +1,362 @@
+#!/usr/bin/env fish
+# Cognitive Ecosystem - Initialization Script
+# Creates the essential structure for your knowledge system
+
+# Configuration
+set CURRENT_DIR (pwd)
+set TEMPLATES_PATH "$CURRENT_DIR/.templates"
+set CURRENT_DATE (date +%Y-%m-%d)
+set DEFAULT_EDITOR "nvim" # Change to your preferred editor
+
+# Colors for prettier output
+set GREEN '\033[0;32m'
+set BLUE '\033[0;34m'
+set YELLOW '\033[0;33m'
+set RED '\033[0;31m'
+set NC '\033[0m' # No Color
+
+function log_step
+    echo -e "$BLUE→ $argv$NC"
+end
+
+function log_done
+    echo -e "$GREEN✓ $argv$NC"
+end
+
+function log_warn
+    echo -e "$YELLOW! $argv$NC"
+end
+
+function log_error
+    echo -e "$RED✗ $argv$NC"
+end
+
+# Prompt for username
+log_step "Please enter your username for the seed file:"
+read -l USERNAME
+if test -z "$USERNAME"
+    set USERNAME "user"
+    log_warn "No username provided, using 'user' as default"
+else
+    log_done "Using username: $USERNAME"
+end
+
+# Safety check - confirm if critical directories already exist
+if test -d "$CURRENT_DIR/journal" -o -d "$CURRENT_DIR/.templates"
+    log_warn "Some system directories already exist in: $CURRENT_DIR"
+    read -l -P "Continue and potentially overwrite existing files? (y/N) " confirm
+    
+    if test "$confirm" != "y" -a "$confirm" != "Y"
+        log_error "Initialization aborted by user"
+        exit 1
+    end
+end
+
+# Create basic README
+log_step "Creating README.md..."
+echo "# Cognitive Ecosystem" > "$CURRENT_DIR/README.md"
+echo "" >> "$CURRENT_DIR/README.md"
+echo "A personal knowledge management system designed for deep integration of ideas, code, and resources." >> "$CURRENT_DIR/README.md"
+log_done "README created"
+
+# Create all necessary directories
+log_step "Creating directory structure..."
+# Main directories
+mkdir -p "$CURRENT_DIR/journal/daily"
+mkdir -p "$CURRENT_DIR/journal/weekly"
+mkdir -p "$CURRENT_DIR/journal/monthly"
+mkdir -p "$CURRENT_DIR/journal/quarterly"
+mkdir -p "$CURRENT_DIR/journal/yearly"
+mkdir -p "$CURRENT_DIR/projects"
+mkdir -p "$CURRENT_DIR/people"
+mkdir -p "$CURRENT_DIR/knowledge"
+mkdir -p "$CURRENT_DIR/notebooks"
+mkdir -p "$CURRENT_DIR/code"
+mkdir -p "$CURRENT_DIR/resources"
+mkdir -p "$TEMPLATES_PATH"
+log_done "Directory structure created"
+
+# Create seed node template
+log_step "Creating seed node template..."
+set SEED_TEMPLATE "$TEMPLATES_PATH/01-seed-node.md"
+echo "---" > $SEED_TEMPLATE
+echo "aliases: [\"Home\", \"Hub\", \"Seed\"]" >> $SEED_TEMPLATE
+echo "tags: [system/core]" >> $SEED_TEMPLATE
+echo "created: $CURRENT_DATE" >> $SEED_TEMPLATE
+echo "---" >> $SEED_TEMPLATE
+echo "" >> $SEED_TEMPLATE
+echo "# Personal Seed Node" >> $SEED_TEMPLATE
+echo "" >> $SEED_TEMPLATE
+echo "## Input Stream" >> $SEED_TEMPLATE
+echo "<!-- Capture your thoughts here without worrying about organization -->" >> $SEED_TEMPLATE
+echo "" >> $SEED_TEMPLATE
+echo "" >> $SEED_TEMPLATE
+echo "## Navigation" >> $SEED_TEMPLATE
+echo "<!-- Core links to primary areas -->" >> $SEED_TEMPLATE
+echo "- [[journal/00-index|Journal]]" >> $SEED_TEMPLATE
+echo "- [[projects/00-index|Projects]]" >> $SEED_TEMPLATE
+echo "- [[people/00-index|People]]" >> $SEED_TEMPLATE
+echo "- [[knowledge/00-index|Knowledge]]" >> $SEED_TEMPLATE
+echo "- [[notebooks/00-index|Notebooks]]" >> $SEED_TEMPLATE
+echo "- [[code/00-index|Code]]" >> $SEED_TEMPLATE
+echo "- [[resources/00-index|Resources]]" >> $SEED_TEMPLATE
+echo "" >> $SEED_TEMPLATE
+echo "## Current Focus" >> $SEED_TEMPLATE
+echo "<!-- What needs your attention right now -->" >> $SEED_TEMPLATE
+echo "" >> $SEED_TEMPLATE
+log_done "Seed node template created"
+
+# Create daily note template
+log_step "Creating daily note template..."
+set DAILY_TEMPLATE "$TEMPLATES_PATH/10-daily-note.md"
+echo "---" > $DAILY_TEMPLATE
+echo "tags: [journal/daily]" >> $DAILY_TEMPLATE
+echo "date: {{date}}" >> $DAILY_TEMPLATE
+echo "---" >> $DAILY_TEMPLATE
+echo "# {{date_pretty}}" >> $DAILY_TEMPLATE
+echo "" >> $DAILY_TEMPLATE
+echo "## Morning Thoughts" >> $DAILY_TEMPLATE
+echo "" >> $DAILY_TEMPLATE
+echo "## Ideas & Notes" >> $DAILY_TEMPLATE
+echo "" >> $DAILY_TEMPLATE
+echo "## Evening Reflection" >> $DAILY_TEMPLATE
+echo "" >> $DAILY_TEMPLATE
+log_done "Daily note template created"
+
+# Create project note template
+log_step "Creating project note template..."
+set PROJECT_TEMPLATE "$TEMPLATES_PATH/20-project-note.md"
+echo "---" > $PROJECT_TEMPLATE
+echo "tags: [project]" >> $PROJECT_TEMPLATE
+echo "status: idea" >> $PROJECT_TEMPLATE
+echo "started: {{date}}" >> $PROJECT_TEMPLATE
+echo "---" >> $PROJECT_TEMPLATE
+echo "# {{title}}" >> $PROJECT_TEMPLATE
+echo "" >> $PROJECT_TEMPLATE
+echo "## Purpose" >> $PROJECT_TEMPLATE
+echo "" >> $PROJECT_TEMPLATE
+echo "## Current Status" >> $PROJECT_TEMPLATE
+echo "" >> $PROJECT_TEMPLATE
+echo "## Next Steps" >> $PROJECT_TEMPLATE
+echo "" >> $PROJECT_TEMPLATE
+log_done "Project template created"
+
+# Create knowledge note template
+log_step "Creating knowledge note template..."
+set KNOWLEDGE_TEMPLATE "$TEMPLATES_PATH/30-knowledge-note.md"
+echo "---" > $KNOWLEDGE_TEMPLATE
+echo "tags: [knowledge]" >> $KNOWLEDGE_TEMPLATE
+echo "created: {{date}}" >> $KNOWLEDGE_TEMPLATE
+echo "---" >> $KNOWLEDGE_TEMPLATE
+echo "# {{title}}" >> $KNOWLEDGE_TEMPLATE
+echo "" >> $KNOWLEDGE_TEMPLATE
+echo "## Overview" >> $KNOWLEDGE_TEMPLATE
+echo "" >> $KNOWLEDGE_TEMPLATE
+echo "## Key Concepts" >> $KNOWLEDGE_TEMPLATE
+echo "" >> $KNOWLEDGE_TEMPLATE
+echo "## Connections" >> $KNOWLEDGE_TEMPLATE
+echo "" >> $KNOWLEDGE_TEMPLATE
+log_done "Knowledge template created"
+
+# Create .env file template
+log_step "Creating .env file template..."
+set ENV_TEMPLATE "$TEMPLATES_PATH/50-env.template"
+echo "# Cognitive Ecosystem Configuration" > $ENV_TEMPLATE
+echo "" >> $ENV_TEMPLATE
+echo "# API Keys" >> $ENV_TEMPLATE
+echo "OPENAI_API_KEY=" >> $ENV_TEMPLATE
+echo "ANTHROPIC_API_KEY=" >> $ENV_TEMPLATE
+echo "" >> $ENV_TEMPLATE
+echo "# Model Configuration" >> $ENV_TEMPLATE
+echo "DEFAULT_LLM_PROVIDER=anthropic" >> $ENV_TEMPLATE
+echo "DEFAULT_LLM_MODEL=claude-3-7-sonnet-20250219" >> $ENV_TEMPLATE
+echo "DEFAULT_EMBEDDING_MODEL=text-embedding-3-large" >> $ENV_TEMPLATE
+echo "" >> $ENV_TEMPLATE
+echo "# System Settings" >> $ENV_TEMPLATE
+echo "LOG_LEVEL=info" >> $ENV_TEMPLATE
+echo "ENABLE_AUTONOMOUS_AGENTS=false" >> $ENV_TEMPLATE
+log_done ".env template created"
+
+# Create basic .gitignore
+log_step "Creating .gitignore..."
+echo ".env" > "$CURRENT_DIR/.gitignore"
+echo ".DS_Store" >> "$CURRENT_DIR/.gitignore"
+echo "__pycache__/" >> "$CURRENT_DIR/.gitignore"
+echo "*.pyc" >> "$CURRENT_DIR/.gitignore"
+log_done ".gitignore created"
+
+# Create initial seed node
+log_step "Creating seed node..."
+set SEED_NODE "$CURRENT_DIR/people/01-seed-$USERNAME.md"
+cat "$TEMPLATES_PATH/01-seed-node.md" > $SEED_NODE
+log_done "Seed node created at $SEED_NODE"
+
+# Create today's daily note
+log_step "Creating today's daily note..."
+set TODAY_NOTE "$CURRENT_DIR/journal/daily/$CURRENT_DATE.md"
+cat "$TEMPLATES_PATH/10-daily-note.md" | sed "s/{{date}}/$CURRENT_DATE/g" | sed "s/{{date_pretty}}/"(date '+%A, %B %-d, %Y')"/g" > $TODAY_NOTE
+log_done "Today's note created at $TODAY_NOTE"
+
+# Create index files
+log_step "Creating index files..."
+# Journal index
+set JOURNAL_INDEX "$CURRENT_DIR/journal/00-index.md"
+echo "# Journal" > $JOURNAL_INDEX
+echo "" >> $JOURNAL_INDEX
+echo "## Daily Entries" >> $JOURNAL_INDEX
+echo "- [[$CURRENT_DATE]] (Today)" >> $JOURNAL_INDEX
+echo "" >> $JOURNAL_INDEX
+echo "## Time Periods" >> $JOURNAL_INDEX
+echo "- [[weekly/00-index|Weekly Reviews]]" >> $JOURNAL_INDEX
+echo "- [[monthly/00-index|Monthly Reviews]]" >> $JOURNAL_INDEX
+echo "- [[quarterly/00-index|Quarterly Reviews]]" >> $JOURNAL_INDEX
+echo "- [[yearly/00-index|Yearly Reviews]]" >> $JOURNAL_INDEX
+echo "" >> $JOURNAL_INDEX
+
+# Journal sub-indexes
+echo "# Weekly Reviews" > "$CURRENT_DIR/journal/weekly/00-index.md"
+echo "" >> "$CURRENT_DIR/journal/weekly/00-index.md"
+echo "# Monthly Reviews" > "$CURRENT_DIR/journal/monthly/00-index.md"
+echo "" >> "$CURRENT_DIR/journal/monthly/00-index.md"
+echo "# Quarterly Reviews" > "$CURRENT_DIR/journal/quarterly/00-index.md"
+echo "" >> "$CURRENT_DIR/journal/quarterly/00-index.md"
+echo "# Yearly Reviews" > "$CURRENT_DIR/journal/yearly/00-index.md"
+echo "" >> "$CURRENT_DIR/journal/yearly/00-index.md"
+
+# Projects index
+echo "# Projects" > "$CURRENT_DIR/projects/00-index.md"
+echo "" >> "$CURRENT_DIR/projects/00-index.md"
+echo "## Active Projects" >> "$CURRENT_DIR/projects/00-index.md"
+echo "" >> "$CURRENT_DIR/projects/00-index.md"
+
+# People index
+echo "# People" > "$CURRENT_DIR/people/00-index.md"
+echo "" >> "$CURRENT_DIR/people/00-index.md"
+echo "## Connections" >> "$CURRENT_DIR/people/00-index.md"
+echo "- [[01-seed-$USERNAME|$USERNAME (Me)]]" >> "$CURRENT_DIR/people/00-index.md"
+echo "" >> "$CURRENT_DIR/people/00-index.md"
+
+# Knowledge index
+echo "# Knowledge" > "$CURRENT_DIR/knowledge/00-index.md"
+echo "" >> "$CURRENT_DIR/knowledge/00-index.md"
+echo "## Domains" >> "$CURRENT_DIR/knowledge/00-index.md"
+echo "" >> "$CURRENT_DIR/knowledge/00-index.md"
+
+# Notebooks index
+echo "# Notebooks" > "$CURRENT_DIR/notebooks/00-index.md"
+echo "" >> "$CURRENT_DIR/notebooks/00-index.md"
+echo "## Experiments" >> "$CURRENT_DIR/notebooks/00-index.md"
+echo "" >> "$CURRENT_DIR/notebooks/00-index.md"
+
+# Code index
+echo "# Code" > "$CURRENT_DIR/code/00-index.md"
+echo "" >> "$CURRENT_DIR/code/00-index.md"
+echo "## Components" >> "$CURRENT_DIR/code/00-index.md"
+echo "" >> "$CURRENT_DIR/code/00-index.md"
+
+# Resources index
+echo "# Resources" > "$CURRENT_DIR/resources/00-index.md"
+echo "" >> "$CURRENT_DIR/resources/00-index.md"
+echo "## Papers" >> "$CURRENT_DIR/resources/00-index.md"
+echo "" >> "$CURRENT_DIR/resources/00-index.md"
+log_done "Index files created"
+
+# Create .env file from template
+log_step "Creating .env file..."
+set ENV_FILE "$CURRENT_DIR/.env"
+cp "$TEMPLATES_PATH/50-env.template" "$ENV_FILE"
+log_done ".env file created"
+
+# Set up fish abbreviation directly in current shell and in config
+log_step "Setting up fish abbreviation..."
+set REPO_PATH (realpath $CURRENT_DIR)
+
+# Create the abbreviation in the current shell
+abbr -a s "cd \"$REPO_PATH\" && $DEFAULT_EDITOR \"people/01-seed-$USERNAME.md\""
+
+# Also add it to the config file if not already there
+if not contains "abbr -Ua s" ~/.config/fish/config.fish
+    echo "" >> ~/.config/fish/config.fish
+    echo "# Cognitive Ecosystem - quick access to seed node" >> ~/.config/fish/config.fish
+    echo "abbr -Ua s 'cd \"$REPO_PATH\" && $DEFAULT_EDITOR \"people/01-seed-$USERNAME.md\"'" >> ~/.config/fish/config.fish
+    log_done "Added abbreviation 's' to fish config and current shell"
+else
+    log_warn "Abbreviation 's' already exists in fish config"
+    log_done "Added abbreviation 's' to current shell only"
+end
+
+# Create next steps document
+log_step "Creating next steps document..."
+set NEXT_STEPS "$CURRENT_DIR/00-NEXT-STEPS.md"
+echo "# Next Steps for Your Cognitive Ecosystem" > $NEXT_STEPS
+echo "" >> $NEXT_STEPS
+echo "Now that you have your basic structure in place, here are some suggested next steps:" >> $NEXT_STEPS
+echo "" >> $NEXT_STEPS
+echo "## Immediate Actions" >> $NEXT_STEPS
+echo "" >> $NEXT_STEPS
+echo "1. **Initialize Git Repository**" >> $NEXT_STEPS
+echo "   ```bash" >> $NEXT_STEPS
+echo "   git init" >> $NEXT_STEPS
+echo "   git add ." >> $NEXT_STEPS
+echo "   git commit -m \"Initial commit: Cognitive Ecosystem seed\"" >> $NEXT_STEPS
+echo "   ```" >> $NEXT_STEPS
+echo "" >> $NEXT_STEPS
+echo "2. **Set Up Obsidian**" >> $NEXT_STEPS
+echo "   - Open this folder in Obsidian" >> $NEXT_STEPS
+echo "   - Configure graph view for better visualization" >> $NEXT_STEPS
+echo "   - Consider useful plugins like Dataview or Calendar" >> $NEXT_STEPS
+echo "" >> $NEXT_STEPS
+echo "3. **Begin Journal Practice**" >> $NEXT_STEPS
+echo "   - Start using the daily journal for note-taking" >> $NEXT_STEPS
+echo "   - Use the seed node as your dashboard" >> $NEXT_STEPS
+echo "   - Begin organizing knowledge as it emerges" >> $NEXT_STEPS
+echo "" >> $NEXT_STEPS
+echo "## Development Paths" >> $NEXT_STEPS
+echo "" >> $NEXT_STEPS
+echo "1. **Basic CLI Tool**" >> $NEXT_STEPS
+echo "   - Create a simple Python CLI in the code directory" >> $NEXT_STEPS
+echo "   - Implement commands for common operations" >> $NEXT_STEPS
+echo "   - Add FZF integration for navigation" >> $NEXT_STEPS
+echo "" >> $NEXT_STEPS
+echo "2. **Resource Processing**" >> $NEXT_STEPS
+echo "   - Set up a pipeline for processing PDFs" >> $NEXT_STEPS
+echo "   - Implement YouTube transcript extraction" >> $NEXT_STEPS
+echo "   - Create a system for code documentation" >> $NEXT_STEPS
+echo "" >> $NEXT_STEPS
+echo "3. **Agent Framework**" >> $NEXT_STEPS
+echo "   - Implement a basic receptionist agent" >> $NEXT_STEPS
+echo "   - Set up vector storage for embeddings" >> $NEXT_STEPS
+echo "   - Create a simple chat interface" >> $NEXT_STEPS
+echo "" >> $NEXT_STEPS
+echo "## File Numbering Convention" >> $NEXT_STEPS
+echo "" >> $NEXT_STEPS
+echo "The system uses a numerical prefix convention for organizing files:" >> $NEXT_STEPS
+echo "" >> $NEXT_STEPS
+echo "- **00-**: Index files that provide an overview of a directory" >> $NEXT_STEPS
+echo "- **01-09**: Primary/core files (e.g., seed node)" >> $NEXT_STEPS
+echo "- **10-49**: Standard content files" >> $NEXT_STEPS
+echo "- **50-99**: Configuration and system files" >> $NEXT_STEPS
+echo "" >> $NEXT_STEPS
+echo "The only files without numerical prefixes are journal entries, which use date-based naming." >> $NEXT_STEPS
+echo "" >> $NEXT_STEPS
+echo "## System Evolution" >> $NEXT_STEPS
+echo "" >> $NEXT_STEPS
+echo "As your system grows, consider:" >> $NEXT_STEPS
+echo "" >> $NEXT_STEPS
+echo "- **Git Hooks** for automation" >> $NEXT_STEPS
+echo "- **Dashboard Development** for system visibility" >> $NEXT_STEPS
+echo "- **Integration with External Tools** like tmux and neovim" >> $NEXT_STEPS
+echo "- **Autonomous Processing** for knowledge metabolism" >> $NEXT_STEPS
+echo "" >> $NEXT_STEPS
+echo "Remember that the system should grow organically based on your actual usage patterns." >> $NEXT_STEPS
+echo "Focus on establishing consistent practices before implementing complex automations." >> $NEXT_STEPS
+log_done "Next steps document created"
+
+echo ""
+log_done "Initialization complete! Your cognitive ecosystem is ready."
+echo ""
+echo -e "$GREEN""To access your seed node, type 's' (works in current shell)""$NC"
+echo -e "$BLUE""Or navigate to: $SEED_NODE""$NC"
+echo ""
+echo -e "$YELLOW""See 00-NEXT-STEPS.md for suggested actions to continue development""$NC"
+echo ""
diff --git a/init.sh b/init.sh
new file mode 100644
index 0000000..4791538
--- /dev/null
+++ b/init.sh
@@ -0,0 +1,368 @@
+#!/usr/bin/env bash
+# Cognitive Ecosystem - Initialization Script
+# Creates the essential structure for your knowledge system
+
+# Configuration
+CURRENT_DIR=$(pwd)
+TEMPLATES_PATH="$CURRENT_DIR/.templates"
+CURRENT_DATE=$(date +%Y-%m-%d)
+DEFAULT_EDITOR="nvim" # Change to your preferred editor
+
+# Colors for prettier output
+GREEN='\033[0;32m'
+BLUE='\033[0;34m'
+YELLOW='\033[0;33m'
+RED='\033[0;31m'
+NC='\033[0m' # No Color
+
+function log_step() {
+    echo -e "${BLUE}→ $1${NC}"
+}
+
+function log_done() {
+    echo -e "${GREEN}✓ $1${NC}"
+}
+
+function log_warn() {
+    echo -e "${YELLOW}! $1${NC}"
+}
+
+function log_error() {
+    echo -e "${RED}✗ $1${NC}"
+}
+
+# Prompt for username
+log_step "Please enter your username for the seed file:"
+read USERNAME
+if [ -z "$USERNAME" ]; then
+    USERNAME="user"
+    log_warn "No username provided, using 'user' as default"
+else
+    log_done "Using username: $USERNAME"
+fi
+
+# Safety check - confirm if critical directories already exist
+if [ -d "$CURRENT_DIR/journal" ] || [ -d "$CURRENT_DIR/.templates" ]; then
+    log_warn "Some system directories already exist in: $CURRENT_DIR"
+    read -p "Continue and potentially overwrite existing files? (y/N) " confirm
+    
+    if [ "$confirm" != "y" ] && [ "$confirm" != "Y" ]; then
+        log_error "Initialization aborted by user"
+        exit 1
+    fi
+fi
+
+# Create basic README
+log_step "Creating README.md..."
+echo "# Cognitive Ecosystem" > "$CURRENT_DIR/README.md"
+echo "" >> "$CURRENT_DIR/README.md"
+echo "A personal knowledge management system designed for deep integration of ideas, code, and resources." >> "$CURRENT_DIR/README.md"
+log_done "README created"
+
+# Create all necessary directories
+log_step "Creating directory structure..."
+# Main directories
+mkdir -p "$CURRENT_DIR/journal/daily"
+mkdir -p "$CURRENT_DIR/journal/weekly"
+mkdir -p "$CURRENT_DIR/journal/monthly"
+mkdir -p "$CURRENT_DIR/journal/quarterly"
+mkdir -p "$CURRENT_DIR/journal/yearly"
+mkdir -p "$CURRENT_DIR/projects"
+mkdir -p "$CURRENT_DIR/people"
+mkdir -p "$CURRENT_DIR/knowledge"
+mkdir -p "$CURRENT_DIR/notebooks"
+mkdir -p "$CURRENT_DIR/code"
+mkdir -p "$CURRENT_DIR/resources"
+mkdir -p "$TEMPLATES_PATH"
+log_done "Directory structure created"
+
+# Create seed node template
+log_step "Creating seed node template..."
+SEED_TEMPLATE="$TEMPLATES_PATH/01-seed-node.md"
+echo "---" > "$SEED_TEMPLATE"
+echo "aliases: [\"Home\", \"Hub\", \"Seed\"]" >> "$SEED_TEMPLATE"
+echo "tags: [system/core]" >> "$SEED_TEMPLATE"
+echo "created: $CURRENT_DATE" >> "$SEED_TEMPLATE"
+echo "---" >> "$SEED_TEMPLATE"
+echo "" >> "$SEED_TEMPLATE"
+echo "# Personal Seed Node" >> "$SEED_TEMPLATE"
+echo "" >> "$SEED_TEMPLATE"
+echo "## Input Stream" >> "$SEED_TEMPLATE"
+echo "<!-- Capture your thoughts here without worrying about organization -->" >> "$SEED_TEMPLATE"
+echo "" >> "$SEED_TEMPLATE"
+echo "" >> "$SEED_TEMPLATE"
+echo "## Navigation" >> "$SEED_TEMPLATE"
+echo "<!-- Core links to primary areas -->" >> "$SEED_TEMPLATE"
+echo "- [[journal/00-index|Journal]]" >> "$SEED_TEMPLATE"
+echo "- [[projects/00-index|Projects]]" >> "$SEED_TEMPLATE"
+echo "- [[people/00-index|People]]" >> "$SEED_TEMPLATE"
+echo "- [[knowledge/00-index|Knowledge]]" >> "$SEED_TEMPLATE"
+echo "- [[notebooks/00-index|Notebooks]]" >> "$SEED_TEMPLATE"
+echo "- [[code/00-index|Code]]" >> "$SEED_TEMPLATE"
+echo "- [[resources/00-index|Resources]]" >> "$SEED_TEMPLATE"
+echo "" >> "$SEED_TEMPLATE"
+echo "## Current Focus" >> "$SEED_TEMPLATE"
+echo "<!-- What needs your attention right now -->" >> "$SEED_TEMPLATE"
+echo "" >> "$SEED_TEMPLATE"
+log_done "Seed node template created"
+
+# Create daily note template
+log_step "Creating daily note template..."
+DAILY_TEMPLATE="$TEMPLATES_PATH/10-daily-note.md"
+echo "---" > "$DAILY_TEMPLATE"
+echo "tags: [journal/daily]" >> "$DAILY_TEMPLATE"
+echo "date: {{date}}" >> "$DAILY_TEMPLATE"
+echo "---" >> "$DAILY_TEMPLATE"
+echo "# {{date_pretty}}" >> "$DAILY_TEMPLATE"
+echo "" >> "$DAILY_TEMPLATE"
+echo "## Morning Thoughts" >> "$DAILY_TEMPLATE"
+echo "" >> "$DAILY_TEMPLATE"
+echo "## Ideas & Notes" >> "$DAILY_TEMPLATE"
+echo "" >> "$DAILY_TEMPLATE"
+echo "## Evening Reflection" >> "$DAILY_TEMPLATE"
+echo "" >> "$DAILY_TEMPLATE"
+log_done "Daily note template created"
+
+# Create project note template
+log_step "Creating project note template..."
+PROJECT_TEMPLATE="$TEMPLATES_PATH/20-project-note.md"
+echo "---" > "$PROJECT_TEMPLATE"
+echo "tags: [project]" >> "$PROJECT_TEMPLATE"
+echo "status: idea" >> "$PROJECT_TEMPLATE"
+echo "started: {{date}}" >> "$PROJECT_TEMPLATE"
+echo "---" >> "$PROJECT_TEMPLATE"
+echo "# {{title}}" >> "$PROJECT_TEMPLATE"
+echo "" >> "$PROJECT_TEMPLATE"
+echo "## Purpose" >> "$PROJECT_TEMPLATE"
+echo "" >> "$PROJECT_TEMPLATE"
+echo "## Current Status" >> "$PROJECT_TEMPLATE"
+echo "" >> "$PROJECT_TEMPLATE"
+echo "## Next Steps" >> "$PROJECT_TEMPLATE"
+echo "" >> "$PROJECT_TEMPLATE"
+log_done "Project template created"
+
+# Create knowledge note template
+log_step "Creating knowledge note template..."
+KNOWLEDGE_TEMPLATE="$TEMPLATES_PATH/30-knowledge-note.md"
+echo "---" > "$KNOWLEDGE_TEMPLATE"
+echo "tags: [knowledge]" >> "$KNOWLEDGE_TEMPLATE"
+echo "created: {{date}}" >> "$KNOWLEDGE_TEMPLATE"
+echo "---" >> "$KNOWLEDGE_TEMPLATE"
+echo "# {{title}}" >> "$KNOWLEDGE_TEMPLATE"
+echo "" >> "$KNOWLEDGE_TEMPLATE"
+echo "## Overview" >> "$KNOWLEDGE_TEMPLATE"
+echo "" >> "$KNOWLEDGE_TEMPLATE"
+echo "## Key Concepts" >> "$KNOWLEDGE_TEMPLATE"
+echo "" >> "$KNOWLEDGE_TEMPLATE"
+echo "## Connections" >> "$KNOWLEDGE_TEMPLATE"
+echo "" >> "$KNOWLEDGE_TEMPLATE"
+log_done "Knowledge template created"
+
+# Create .env file template
+log_step "Creating .env file template..."
+ENV_TEMPLATE="$TEMPLATES_PATH/50-env.template"
+echo "# Cognitive Ecosystem Configuration" > "$ENV_TEMPLATE"
+echo "" >> "$ENV_TEMPLATE"
+echo "# API Keys" >> "$ENV_TEMPLATE"
+echo "OPENAI_API_KEY=" >> "$ENV_TEMPLATE"
+echo "ANTHROPIC_API_KEY=" >> "$ENV_TEMPLATE"
+echo "" >> "$ENV_TEMPLATE"
+echo "# Model Configuration" >> "$ENV_TEMPLATE"
+echo "DEFAULT_LLM_PROVIDER=anthropic" >> "$ENV_TEMPLATE"
+echo "DEFAULT_LLM_MODEL=claude-3-7-sonnet-20250219" >> "$ENV_TEMPLATE"
+echo "DEFAULT_EMBEDDING_MODEL=text-embedding-3-large" >> "$ENV_TEMPLATE"
+echo "" >> "$ENV_TEMPLATE"
+echo "# System Settings" >> "$ENV_TEMPLATE"
+echo "LOG_LEVEL=info" >> "$ENV_TEMPLATE"
+echo "ENABLE_AUTONOMOUS_AGENTS=false" >> "$ENV_TEMPLATE"
+log_done ".env template created"
+
+# Create basic .gitignore
+log_step "Creating .gitignore..."
+echo ".env" > "$CURRENT_DIR/.gitignore"
+echo ".DS_Store" >> "$CURRENT_DIR/.gitignore"
+echo "__pycache__/" >> "$CURRENT_DIR/.gitignore"
+echo "*.pyc" >> "$CURRENT_DIR/.gitignore"
+log_done ".gitignore created"
+
+# Create initial seed node
+log_step "Creating seed node..."
+SEED_NODE="$CURRENT_DIR/people/01-seed-$USERNAME.md"
+cat "$TEMPLATES_PATH/01-seed-node.md" > "$SEED_NODE"
+log_done "Seed node created at $SEED_NODE"
+
+# Create today's daily note
+log_step "Creating today's daily note..."
+TODAY_NOTE="$CURRENT_DIR/journal/daily/$CURRENT_DATE.md"
+DATE_PRETTY=$(date '+%A, %B %-d, %Y')
+sed "s/{{date}}/$CURRENT_DATE/g" "$TEMPLATES_PATH/10-daily-note.md" | sed "s/{{date_pretty}}/$DATE_PRETTY/g" > "$TODAY_NOTE"
+log_done "Today's note created at $TODAY_NOTE"
+
+# Create index files
+log_step "Creating index files..."
+# Journal index
+JOURNAL_INDEX="$CURRENT_DIR/journal/00-index.md"
+echo "# Journal" > "$JOURNAL_INDEX"
+echo "" >> "$JOURNAL_INDEX"
+echo "## Daily Entries" >> "$JOURNAL_INDEX"
+echo "- [[$CURRENT_DATE]] (Today)" >> "$JOURNAL_INDEX"
+echo "" >> "$JOURNAL_INDEX"
+echo "## Time Periods" >> "$JOURNAL_INDEX"
+echo "- [[weekly/00-index|Weekly Reviews]]" >> "$JOURNAL_INDEX"
+echo "- [[monthly/00-index|Monthly Reviews]]" >> "$JOURNAL_INDEX"
+echo "- [[quarterly/00-index|Quarterly Reviews]]" >> "$JOURNAL_INDEX"
+echo "- [[yearly/00-index|Yearly Reviews]]" >> "$JOURNAL_INDEX"
+echo "" >> "$JOURNAL_INDEX"
+
+# Journal sub-indexes
+echo "# Weekly Reviews" > "$CURRENT_DIR/journal/weekly/00-index.md"
+echo "" >> "$CURRENT_DIR/journal/weekly/00-index.md"
+echo "# Monthly Reviews" > "$CURRENT_DIR/journal/monthly/00-index.md"
+echo "" >> "$CURRENT_DIR/journal/monthly/00-index.md"
+echo "# Quarterly Reviews" > "$CURRENT_DIR/journal/quarterly/00-index.md"
+echo "" >> "$CURRENT_DIR/journal/quarterly/00-index.md"
+echo "# Yearly Reviews" > "$CURRENT_DIR/journal/yearly/00-index.md"
+echo "" >> "$CURRENT_DIR/journal/yearly/00-index.md"
+
+# Projects index
+echo "# Projects" > "$CURRENT_DIR/projects/00-index.md"
+echo "" >> "$CURRENT_DIR/projects/00-index.md"
+echo "## Active Projects" >> "$CURRENT_DIR/projects/00-index.md"
+echo "" >> "$CURRENT_DIR/projects/00-index.md"
+
+# People index
+echo "# People" > "$CURRENT_DIR/people/00-index.md"
+echo "" >> "$CURRENT_DIR/people/00-index.md"
+echo "## Connections" >> "$CURRENT_DIR/people/00-index.md"
+echo "- [[01-seed-$USERNAME|$USERNAME (Me)]]" >> "$CURRENT_DIR/people/00-index.md"
+echo "" >> "$CURRENT_DIR/people/00-index.md"
+
+# Knowledge index
+echo "# Knowledge" > "$CURRENT_DIR/knowledge/00-index.md"
+echo "" >> "$CURRENT_DIR/knowledge/00-index.md"
+echo "## Domains" >> "$CURRENT_DIR/knowledge/00-index.md"
+echo "" >> "$CURRENT_DIR/knowledge/00-index.md"
+
+# Notebooks index
+echo "# Notebooks" > "$CURRENT_DIR/notebooks/00-index.md"
+echo "" >> "$CURRENT_DIR/notebooks/00-index.md"
+echo "## Experiments" >> "$CURRENT_DIR/notebooks/00-index.md"
+echo "" >> "$CURRENT_DIR/notebooks/00-index.md"
+
+# Code index
+echo "# Code" > "$CURRENT_DIR/code/00-index.md"
+echo "" >> "$CURRENT_DIR/code/00-index.md"
+echo "## Components" >> "$CURRENT_DIR/code/00-index.md"
+echo "" >> "$CURRENT_DIR/code/00-index.md"
+
+# Resources index
+echo "# Resources" > "$CURRENT_DIR/resources/00-index.md"
+echo "" >> "$CURRENT_DIR/resources/00-index.md"
+echo "## Papers" >> "$CURRENT_DIR/resources/00-index.md"
+echo "" >> "$CURRENT_DIR/resources/00-index.md"
+log_done "Index files created"
+
+# Create .env file from template
+log_step "Creating .env file..."
+ENV_FILE="$CURRENT_DIR/.env"
+cp "$TEMPLATES_PATH/50-env.template" "$ENV_FILE"
+log_done ".env file created"
+
+# Set up bash alias directly in current shell and in config
+log_step "Setting up bash alias..."
+REPO_PATH=$(realpath "$CURRENT_DIR")
+
+# Create the alias in the current shell
+alias s="cd \"$REPO_PATH\" && $DEFAULT_EDITOR \"people/01-seed-$USERNAME.md\""
+
+# Also add it to the config file if not already there
+BASH_RC="$HOME/.bashrc"
+if [ -f "$HOME/.bash_profile" ]; then
+    BASH_RC="$HOME/.bash_profile"
+fi
+
+if ! grep -q "alias s='cd \"$REPO_PATH\"" "$BASH_RC"; then
+    echo "" >> "$BASH_RC"
+    echo "# Cognitive Ecosystem - quick access to seed node" >> "$BASH_RC"
+    echo "alias s='cd \"$REPO_PATH\" && $DEFAULT_EDITOR \"people/01-seed-$USERNAME.md\"'" >> "$BASH_RC"
+    log_done "Added alias 's' to bash config and current shell"
+else
+    log_warn "Alias 's' already exists in bash config"
+    log_done "Added alias 's' to current shell only"
+fi
+
+# Create next steps document
+log_step "Creating next steps document..."
+NEXT_STEPS="$CURRENT_DIR/00-NEXT-STEPS.md"
+echo "# Next Steps for Your Cognitive Ecosystem" > "$NEXT_STEPS"
+echo "" >> "$NEXT_STEPS"
+echo "Now that you have your basic structure in place, here are some suggested next steps:" >> "$NEXT_STEPS"
+echo "" >> "$NEXT_STEPS"
+echo "## Immediate Actions" >> "$NEXT_STEPS"
+echo "" >> "$NEXT_STEPS"
+echo "1. **Initialize Git Repository**" >> "$NEXT_STEPS"
+echo "   \`\`\`bash" >> "$NEXT_STEPS"
+echo "   git init" >> "$NEXT_STEPS"
+echo "   git add ." >> "$NEXT_STEPS"
+echo "   git commit -m \"Initial commit: Cognitive Ecosystem seed\"" >> "$NEXT_STEPS"
+echo "   \`\`\`" >> "$NEXT_STEPS"
+echo "" >> "$NEXT_STEPS"
+echo "2. **Set Up Obsidian**" >> "$NEXT_STEPS"
+echo "   - Open this folder in Obsidian" >> "$NEXT_STEPS"
+echo "   - Configure graph view for better visualization" >> "$NEXT_STEPS"
+echo "   - Consider useful plugins like Dataview or Calendar" >> "$NEXT_STEPS"
+echo "" >> "$NEXT_STEPS"
+echo "3. **Begin Journal Practice**" >> "$NEXT_STEPS"
+echo "   - Start using the daily journal for note-taking" >> "$NEXT_STEPS"
+echo "   - Use the seed node as your dashboard" >> "$NEXT_STEPS"
+echo "   - Begin organizing knowledge as it emerges" >> "$NEXT_STEPS"
+echo "" >> "$NEXT_STEPS"
+echo "## Development Paths" >> "$NEXT_STEPS"
+echo "" >> "$NEXT_STEPS"
+echo "1. **Basic CLI Tool**" >> "$NEXT_STEPS"
+echo "   - Create a simple Python CLI in the code directory" >> "$NEXT_STEPS"
+echo "   - Implement commands for common operations" >> "$NEXT_STEPS"
+echo "   - Add FZF integration for navigation" >> "$NEXT_STEPS"
+echo "" >> "$NEXT_STEPS"
+echo "2. **Resource Processing**" >> "$NEXT_STEPS"
+echo "   - Set up a pipeline for processing PDFs" >> "$NEXT_STEPS"
+echo "   - Implement YouTube transcript extraction" >> "$NEXT_STEPS"
+echo "   - Create a system for code documentation" >> "$NEXT_STEPS"
+echo "" >> "$NEXT_STEPS"
+echo "3. **Agent Framework**" >> "$NEXT_STEPS"
+echo "   - Implement a basic receptionist agent" >> "$NEXT_STEPS"
+echo "   - Set up vector storage for embeddings" >> "$NEXT_STEPS"
+echo "   - Create a simple chat interface" >> "$NEXT_STEPS"
+echo "" >> "$NEXT_STEPS"
+echo "## File Numbering Convention" >> "$NEXT_STEPS"
+echo "" >> "$NEXT_STEPS"
+echo "The system uses a numerical prefix convention for organizing files:" >> "$NEXT_STEPS"
+echo "" >> "$NEXT_STEPS"
+echo "- **00-**: Index files that provide an overview of a directory" >> "$NEXT_STEPS"
+echo "- **01-09**: Primary/core files (e.g., seed node)" >> "$NEXT_STEPS"
+echo "- **10-49**: Standard content files" >> "$NEXT_STEPS"
+echo "- **50-99**: Configuration and system files" >> "$NEXT_STEPS"
+echo "" >> "$NEXT_STEPS"
+echo "The only files without numerical prefixes are journal entries, which use date-based naming." >> "$NEXT_STEPS"
+echo "" >> "$NEXT_STEPS"
+echo "## System Evolution" >> "$NEXT_STEPS"
+echo "" >> "$NEXT_STEPS"
+echo "As your system grows, consider:" >> "$NEXT_STEPS"
+echo "" >> "$NEXT_STEPS"
+echo "- **Git Hooks** for automation" >> "$NEXT_STEPS"
+echo "- **Dashboard Development** for system visibility" >> "$NEXT_STEPS"
+echo "- **Integration with External Tools** like tmux and neovim" >> "$NEXT_STEPS"
+echo "- **Autonomous Processing** for knowledge metabolism" >> "$NEXT_STEPS"
+echo "" >> "$NEXT_STEPS"
+echo "Remember that the system should grow organically based on your actual usage patterns." >> "$NEXT_STEPS"
+echo "Focus on establishing consistent practices before implementing complex automations." >> "$NEXT_STEPS"
+log_done "Next steps document created"
+
+echo ""
+log_done "Initialization complete! Your cognitive ecosystem is ready."
+echo ""
+echo -e "${GREEN}To access your seed node, type 's' (works in current shell)${NC}"
+echo -e "${BLUE}Or navigate to: $SEED_NODE${NC}"
+echo ""
+echo -e "${YELLOW}See 00-NEXT-STEPS.md for suggested actions to continue development${NC}"
+echo ""