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# =============================================================================
# Knowledge Genome - Makefile v. 0.1.0
# Orchestrates the setup and management of the knowledge base.
# =============================================================================
include config.env
export $(shell sed 's/=.*//' config.env)
.PHONY: setup add-genome status lint clean help
help:
@echo "Available commands:"
@echo " make setup - Full system initialization"
@echo " make add-genome - Register and scaffold a new genome"
@echo " make status - Check submodule and encryption status"
@echo " make lint - Verify schema, privacy flags, and metadata"
lint:
@bash scripts/lint-genomes.sh
setup:
@bash scripts/setup.sh
add-genome:
@if [ -z "$(NAME)" ] || [ -z "$(DESC)" ]; then \
echo "Error: NAME and DESC are required."; \
echo "Usage: make add-genome NAME=my-genome DESC='My description'"; \
exit 1; \
fi
@bash scripts/add-genome.sh "$(NAME)" "$(DESC)"
status:
@echo "--- Master Status ---"
@git submodule status
@echo "--- Encryption Status (First 10 files) ---"
@git-crypt status | head -n 10

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README.md
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# knowledge-genome-orchestrator
# Knowledge Genome System
> A distributed, modular, and secure personal knowledge base architecture.
The **Knowledge Genome System** is a framework designed to manage personal knowledge using a "Master-Genome" architecture. It follows the LLM-Wiki patterns (Karpathy-style) while adding a robust security layer for sensitive data and automated quality control.
---
# Architecture
This project is structured as a **Master Orchestrator** that manages multiple independent **Genomes** via Git Submodules.
## Core Components
### Master Repository
Contains:
* Orchestration scripts
* Global configuration (`config.env`)
* Security templates
### Genomes
Individual specialized repositories (e.g. `genome-dev`, `genome-finance`) that act as standalone units of knowledge.
### Security Layers
#### Physical Security
`git-crypt` encrypts `private/` directories at rest.
#### Logical Security
YAML frontmatter (`private: true`) prevents AI agents from leaking sensitive data during public sessions.
#### Validation Layer
A custom linting engine ensures metadata consistency.
---
# Quick Start
## Prerequisites
Required dependencies:
* `git`
* `git-crypt`
* `curl`
* `jq`
Optional:
* `bw` (Bitwarden CLI) — used for runtime key injection
---
## Initialization
```bash
# 1. Clone the master repository
git clone <master-repo-url> && cd master-knowledge-genome
# 2. Run the full setup
# (checks dependencies, creates master scaffold,
# initializes genomes)
make setup
```
# Management Commands
The system is controlled through a centralized Makefile.
| Command | Description |
| ----------------- | -------------------------------------------------------------- |
| `make setup` | Full system initialization (Master + Registry Genomes). |
| `make add-genome` | Scaffolds and registers a new genome (requires NAME and DESC). |
| `make lint` | Runs the validation suite across all genomes. |
| `make status` | Checks Git status and encryption state for all submodules. |
# Validation & Linting (`make lint`)
The built-in linter ensures that the knowledge base remains machine-readable and secure.
It automatically validates:
## Frontmatter Integrity
Every `.md` file must contain valid YAML headers.
## Domain Consistency
Ensures that a file's domain metadata matches its parent genome.
## Privacy Leak Detection
Critical validation step.
Verifies that any file located in a `/private/` directory contains the flag:
```yaml
private: true
```
This prevents accidental exposure during AI sessions.
## Broken Wiki-Links
Detects dead `[[internal-links]]`.
# Security Model
## Hybrid Privacy Architecture
Each genome is divided into two layers.
### Public Layer
Directories:
```text
raw/public/
wiki/public/
```
Characteristics:
* Plaintext
* Shareable with collaborators
### Private Layer
Directories:
```text
raw/private/
wiki/private/
```
Characteristics:
* Encrypted using AES-256 via `git-crypt`
## Runtime Key Injection
To keep the AI environment secure, encryption keys are never stored on the VM disk.
Instead, the system uses Bitwarden (`bw`) / Vaultwarden for runtime injection.
### Example
```bash
# Unlock a genome using a key stored in Vaultwarden
git-crypt unlock <(
bw get notes "genome-dev key" \
--session "$BW_SESSION" | base64 -d
)
```
# Genome Schema
All wiki documents follow a strict schema to support AI ingestion.
## YAML Frontmatter Schema
```yaml
---
title: "Document Title"
type: entity | concept | source | log
domain: genome-name
private: true/false
last_updated: YYYY-MM-DD
---
```
# Agent Interaction
When starting a session with an AI agent, always declare the privacy context.
## Public Context
```text
PRIVATE_CONTEXT: disabled
```
Behavior:
* The agent ignores all private folders.
## Private Context
```text
PRIVATE_CONTEXT: enabled
```
Behavior:
* The agent processes encrypted data.
* Requires the repository to be unlocked.

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#!/usr/bin/env bash
# =============================================================================
# config.env
# Single Source of Truth for the Knowledge Genome Framework.
# =============================================================================
# --- PROVIDER SELECTION ---
PROVIDER="forgejo" # Options: "forgejo", "github"
# --- FORGEJO CONFIGURATION ---
FORGEJO_URL="https://git.keruhomelab.com"
FORGEJO_USER="keru"
# Note: FORGEJO_TOKEN must be exported in your shell for security.
# --- VAULTWARDEN CONFIGURATION ---
# Used for rendering template instructions
VAULTWARDEN_URL="https://vault.keruhomelab.com"
# --- MASTER REPOSITORY ---
MASTER_REPO="master-knowledge-genome"
GIST_URL="https://gist.github.com/442a6bf555914893e9891c11519de94f.git"
# --- GENOME REGISTRY ---
# Format: "name|description"
GENOMES=(
"genome-dev|Web development, TUI, Angular, software architecture"
"genome-finance|Personal finance, investments, market analysis"
"genome-homelab|Keru infrastructure, network configs, architecture logs"
)
# --- SYSTEM PATHS ---
WORK_DIR="${HOME}/knowledge-genome-setup"
KEYS_DIR="${WORK_DIR}/keys"
# Core directory resolution (DO NOT CHANGE)
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
TEMPLATES_DIR="${SCRIPT_DIR}/templates"
LIB_DIR="${SCRIPT_DIR}/lib"
PROVIDERS_DIR="${SCRIPT_DIR}/providers"

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#!/usr/bin/env bash
# =============================================================================
# lib/deps.sh
# Dependency and environment validation.
# =============================================================================
check_deps() {
local missing=()
local required=(git git-crypt curl jq)
for cmd in "${required[@]}"; do
if ! command -v "$cmd" &>/dev/null; then
missing+=("$cmd")
fi
done
if [[ ${#missing[@]} -gt 0 ]]; then
error "Missing required tools: ${missing[*]}"
echo -e "\nInstall them using your package manager:"
echo " Debian/Ubuntu: sudo apt install ${missing[*]}"
echo " MacOS: brew install ${missing[*]}"
exit 1
fi
success "Environment check passed: all required tools found."
if ! command -v bw &>/dev/null; then
warn "Optional tool 'bw' (Bitwarden CLI) not found. Vaultwarden integration will be manual."
fi
}
check_git_identity() {
if [[ -z "$(git config user.name)" || -z "$(git config user.email)" ]]; then
warn "Git identity not set globally. Scripts will attempt to use local config."
fi
}

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#!/usr/bin/env bash
# =============================================================================
# lib/git-crypt.sh
# git-crypt lifecycle management (init, export, verify).
# =============================================================================
gcrypt_init() {
git-crypt init
success "git-crypt initialized in $(pwd)"
}
gcrypt_export_key() {
local genome_name="$1"
local key_path="${KEYS_DIR}/${genome_name}.key"
mkdir -p "${KEYS_DIR}"
git-crypt export-key "$key_path"
success "Symmetric key exported to: $key_path"
warn "Action required: Store this key in Vaultwarden and remove it from local disk."
}
gcrypt_verify() {
local genome_name="$1"
local key_path="${KEYS_DIR}/${genome_name}.key"
info "Verifying git-crypt status for ${genome_name}..."
git-crypt lock
# Checking if the private marker is still encrypted (binary check)
if file "raw/private/.gitkeep" 2>/dev/null | grep -q "data"; then
success "Encryption verified: private/ directory is protected."
else
warn "Encryption check inconclusive. Please run 'git-crypt status' manually."
fi
[[ -f "$key_path" ]] && git-crypt unlock "$key_path"
}
gcrypt_print_key_instructions() {
local genome_name="$1"
local v_url="${VAULTWARDEN_URL:-https://your-vaultwarden.com}"
echo -e "\n ── ${BOLD}Key Management: ${genome_name}${NC} ──\n"
echo " 1. Encode the key to base64:"
echo " base64 < ${KEYS_DIR}/${genome_name}.key"
echo ""
echo " 2. Save to Vaultwarden (${v_url}):"
echo " Name: \"${genome_name} key\""
echo " Note: <paste the base64 string>"
echo ""
echo " 3. For AI Server / Runtime Injection:"
echo " export BW_SESSION=\$(bw unlock --raw)"
echo " git-crypt unlock <(bw get notes \"${genome_name} key\" --session \"\$BW_SESSION\" | base64 -d)"
}
gcrypt_print_runtime_model() {
echo ""
echo " RUNTIME SECURITY MODEL:"
echo " ─────────────────────────────────────────────────────────────"
echo " On Forgejo (remote):"
echo " raw/private/ and wiki/private/ are opaque AES-256-CTR blobs."
echo " Collaborators without the key see binary in private/,"
echo " plaintext everywhere else. Git handles this gracefully."
echo ""
echo " On your laptop:"
echo " Once unlocked, files are transparently decrypted by the git"
echo " smudge filter. Obsidian reads them as normal Markdown."
echo ""
echo " On the AI VM:"
echo " Same as laptop when unlocked. Use runtime injection (step 5"
echo " above) so the key is never written to disk."
echo ""
echo " Limitation:"
echo " Encryption does NOT protect against a full server compromise"
echo " where an attacker has root access to a machine where the repo"
echo " is already unlocked. Runtime injection mitigates this."
echo " ─────────────────────────────────────────────────────────────"
echo ""
}

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#!/usr/bin/env bash
# =============================================================================
# lib/lint.sh
# Validation logic for Knowledge Genome files.
# =============================================================================
# Validates YAML frontmatter and mandatory fields
lint_markdown_file() {
local file="$1"
local genome_name="$2"
local errors=0
# 1. Check Frontmatter delimiters
if [[ $(head -n 1 "$file") != "---" ]]; then
warn "Missing frontmatter start (---) in: $file"
errors=$((errors + 1))
fi
# 2. Check mandatory fields
local mandatory_fields=("title:" "type:" "domain:")
for field in "${mandatory_fields[@]}"; do
if ! grep -q "^${field}" "$file"; then
warn "Missing mandatory field '${field}' in: $file"
errors=$((errors + 1))
fi
done
# 3. Check if domain matches the genome name
if grep -q "^domain:" "$file" && ! grep -q "^domain: ${genome_name}" "$file"; then
warn "Domain mismatch in $file (expected ${genome_name})"
errors=$((errors + 1))
fi
return $errors
}
# Ensures files in private/ directories have the 'private: true' flag
check_privacy_consistency() {
local file="$1"
local errors=0
if [[ "$file" == *"/private/"* ]]; then
if ! grep -q "^private: true" "$file"; then
error "Privacy Leak: $file is in a private folder but lacks 'private: true' metadata."
errors=$((errors + 1))
fi
else
if grep -q "^private: true" "$file"; then
warn "Metadata Mismatch: $file is marked private but located in a public directory."
# We count this as a warning unless you want to force strict isolation
fi
fi
return $errors
}
# Basic check for internal wiki-links [[target]]
check_broken_links() {
local file="$1"
local base_dir
base_dir=$(dirname "$file")
# Extract links, stripping aliases: [[Link|Alias]] -> Link
local links
links=$(grep -oP '\[\[\K[^\]]+' "$file" | cut -d'|' -f1)
for link in $links; do
local target="$link"
[[ "$target" != *.md ]] && target="${target}.md"
# Simple relative check
if [[ ! -f "${base_dir}/${target}" && ! -f "${base_dir}/../${target}" ]]; then
# Only a warning as links might point to other genomes or deep structures
warn "Potential broken link: [[$link]] in $file"
fi
done
}

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#!/usr/bin/env bash
# =============================================================================
# lib/output.sh
# Terminal output helpers: colors, log levels, and step banners.
# =============================================================================
if [[ -t 1 ]]; then
GREEN='\033[0;32m'
YELLOW='\033[1;33m'
CYAN='\033[0;36m'
RED='\033[0;31m'
BOLD='\033[1m'
NC='\033[0m'
else
GREEN='' YELLOW='' CYAN='' RED='' BOLD='' NC=''
fi
info() { echo -e "${CYAN}[INFO]${NC} $*"; }
success() { echo -e "${GREEN}[OK]${NC} $*"; }
warn() { echo -e "${YELLOW}[WARN]${NC} $*"; }
error() { echo -e "${RED}[ERROR]${NC} $*" >&2; }
step() { echo -e "\n${BOLD}${YELLOW}━━━ $* ━━━${NC}"; }
box() {
local max_len=0
for line in "$@"; do
[[ ${#line} -gt $max_len ]] && max_len=${#line}
done
local border
border=$(printf '─%.0s' $(seq 1 $((max_len + 2))))
echo -e "${CYAN}┌${border}┐${NC}"
for line in "$@"; do
printf "${CYAN}│${NC} %-${max_len}s ${CYAN}│${NC}\n" "$line"
done
echo -e "${CYAN}└${border}┘${NC}"
}

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#!/usr/bin/env bash
# =============================================================================
# lib/scaffold.sh
# Directory structure creation and template rendering engine.
# =============================================================================
render_template() {
local template_file="$1"
local output_file="$2"
[[ ! -f "$template_file" ]] && { error "Template not found: ${template_file}"; exit 1; }
local content
content=$(cat "$template_file")
# Placeholder replacement
content="${content//\{\{GENOME_NAME\}\}/${GENOME_NAME}}"
content="${content//\{\{GENOME_NAME_UPPER\}\}/${GENOME_NAME^^}}"
content="${content//\{\{GENOME_DESC\}\}/${GENOME_DESC}}"
content="${content//\{\{FORGEJO_URL\}\}/${FORGEJO_URL}}"
content="${content//\{\{FORGEJO_USER\}\}/${FORGEJO_USER}}"
content="${content//\{\{VAULTWARDEN_URL\}\}/${VAULTWARDEN_URL}}"
content="${content//\{\{MASTER_REPO\}\}/${MASTER_REPO}}"
content="${content//\{\{DATE\}\}/$(date +%Y-%m-%d)}"
mkdir -p "$(dirname "$output_file")"
printf '%s\n' "$content" > "$output_file"
}
scaffold_genome() {
local base="$1"
local dirs=(
"raw/articles" "raw/transcripts" "raw/code-packs" "raw/assets" "raw/private"
"wiki/sources" "wiki/entities" "wiki/concepts" "wiki/queries" "wiki/private"
)
info "Building directory structure in ${base}..."
for dir in "${dirs[@]}"; do
mkdir -p "${base}/${dir}"
touch "${base}/${dir}/.gitkeep"
done
# Core templates
render_template "${TEMPLATES_DIR}/gitattributes" "${base}/.gitattributes"
render_template "${TEMPLATES_DIR}/gitignore" "${base}/.gitignore"
render_template "${TEMPLATES_DIR}/agents-genome.md" "${base}/AGENTS.md"
render_template "${TEMPLATES_DIR}/wiki-index.md" "${base}/wiki/index.md"
render_template "${TEMPLATES_DIR}/wiki-log.md" "${base}/wiki/log.md"
success "Scaffold completed for genome: ${GENOME_NAME}"
}
install_precommit_hook() {
local repo_path="$1"
local hook_path="${repo_path}/.git/hooks/pre-commit"
cp "${TEMPLATES_DIR}/pre-commit.sh" "$hook_path"
chmod +x "$hook_path"
success "Pre-commit security hook installed at: $hook_path"
}
scaffold_master() {
local base="$1"
render_template "${TEMPLATES_DIR}/agents-master.md" "${base}/AGENTS.md"
render_template "${TEMPLATES_DIR}/readme-master.md" "${base}/README.md"
success "Master repository scaffold completed."
}

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#!/usr/bin/env bash
# =============================================================================
# providers/forgejo.sh
# Forgejo REST API provider implementation.
# =============================================================================
provider_name() {
echo "Forgejo (${FORGEJO_URL})"
}
# ---------------------------------------------------------------------------
# provider_create_repo <name> <description> <private: true|false>
# ---------------------------------------------------------------------------
provider_create_repo() {
local name="$1"
local desc="$2"
local private="$3"
local http_code
http_code=$(curl -s -o /dev/null -w "%{http_code}" \
-H "Authorization: token ${FORGEJO_TOKEN}" \
-H "Content-Type: application/json" \
-X POST "${FORGEJO_URL}/api/v1/user/repos" \
-d "{
\"name\": \"${name}\",
\"description\": \"${desc}\",
\"private\": ${private},
\"auto_init\": false
}")
case "$http_code" in
201) success "Repository '${name}' created successfully." ;;
409) info "Repository '${name}' already exists - skipping." ;;
401) error "Unauthorized. Check your FORGEJO_TOKEN."; exit 1 ;;
*) error "Forgejo API returned HTTP ${http_code}. Check connectivity."; exit 1 ;;
esac
}
provider_clone_url() {
echo "${FORGEJO_URL}/${FORGEJO_USER}/${1}.git"
}
provider_ssh_url() {
local host
# Extract hostname by removing protocol and trailing slashes
host=$(echo "${FORGEJO_URL}" | sed -e 's|^[^/]*//||' -e 's|/*$||')
# Using port 222 as default for many homelab Forgejo/Gitea setups
echo "ssh://git@${host}:222/${FORGEJO_USER}/${1}.git"
}
provider_web_url() {
echo "${FORGEJO_URL}/${FORGEJO_USER}/${1}"
}

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#!/usr/bin/env bash
# =============================================================================
# providers/github.sh
# GitHub REST API provider implementation.
# =============================================================================
provider_name() {
echo "GitHub (https://github.com)"
}
_github_namespace() {
echo "${GITHUB_ORG:-$GITHUB_USER}"
}
provider_create_repo() {
local name="$1"
local desc="$2"
local private="$3"
local namespace
namespace=$(_github_namespace)
local endpoint="https://api.github.com/user/repos"
[[ -n "${GITHUB_ORG:-}" ]] && endpoint="https://api.github.com/orgs/${namespace}/repos"
local http_code
http_code=$(curl -s -o /dev/null -w "%{http_code}" \
-H "Authorization: token ${GITHUB_TOKEN}" \
-H "Accept: application/vnd.github.v3+json" \
-X POST "$endpoint" \
-d "{
\"name\": \"${name}\",
\"description\": \"${desc}\",
\"private\": ${private},
\"auto_init\": false
}")
case "$http_code" in
201) success "Repository '${name}' created on GitHub." ;;
422) info "Repository '${name}' already exists - skipping." ;;
*) error "GitHub API returned HTTP ${http_code}. check token/permissions."; exit 1 ;;
esac
}
provider_ssh_url() {
echo "git@github.com:$(_github_namespace)/${1}.git"
}
provider_clone_url() {
echo "https://github.com/$(_github_namespace)/${1}.git"
}
provider_web_url() {
echo "https://github.com/$(_github_namespace)/${1}"
}

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#!/usr/bin/env bash
# =============================================================================
# scripts/add-genome.sh
# Helper to add a single new genome to the existing infrastructure.
# Usage: make add-genome NAME=my-new-genome DESC="Description here"
# =============================================================================
set -euo pipefail
source "lib/output.sh"
source "config.env"
GENOME_NAME="${1:-}"
GENOME_DESC="${2:-}"
if [[ -z "$GENOME_NAME" || -z "$GENOME_DESC" ]]; then
error "Missing arguments."
echo "Usage: $0 <genome-name> <description>"
exit 1
fi
step "Adding New Genome: ${GENOME_NAME}"
# Overwrite the GENOMES array for this session to process only the new one
export GENOMES=("${GENOME_NAME}|${GENOME_DESC}")
# Trigger the standard genome setup logic
bash "scripts/setup-genomes.sh"
success "Genome '${GENOME_NAME}' added and linked successfully!"

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#!/usr/bin/env bash
# =============================================================================
# scripts/lint-genomes.sh
# Executes quality control across all registered genomes.
# =============================================================================
set -euo pipefail
source "lib/output.sh"
source "config.env"
source "lib/lint.sh"
step "Starting Knowledge Genome Linting"
TOTAL_ERRORS=0
# Iterate through genome submodules inside the Master repo
for genome_dir in "${WORK_DIR}/${MASTER_REPO}"/genome-*/; do
[[ -d "$genome_dir" ]] || continue
GENOME_NAME=$(basename "$genome_dir")
info "Auditing genome: ${GENOME_NAME}..."
# Find all .md files, excluding AGENTS.md and external references
while IFS= read -r md_file; do
# Run validations
lint_markdown_file "$md_file" "$GENOME_NAME" || TOTAL_ERRORS=$((TOTAL_ERRORS + $?))
check_privacy_consistency "$md_file" || TOTAL_ERRORS=$((TOTAL_ERRORS + $?))
check_broken_links "$md_file"
done < <(find "$genome_dir" -name "*.md" ! -name "AGENTS.md" ! -path "*/core-karpathy/*")
done
if [[ $TOTAL_ERRORS -eq 0 ]]; then
success "Linting passed: All files are consistent and secure."
else
error "Linting failed: Found ${TOTAL_ERRORS} critical issues."
exit 1
fi

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#!/usr/bin/env bash
# =============================================================================
# scripts/setup-genomes.sh
# Iterates through the GENOMES registry to provision remote and local repos.
# Handles git-crypt initialization and submodule linking.
# =============================================================================
set -euo pipefail
source "lib/output.sh"
source "config.env"
source "lib/scaffold.sh"
source "lib/git-crypt.sh"
source "providers/${PROVIDER}.sh"
step "Processing Genome Registry"
for entry in "${GENOMES[@]}"; do
# Parse name and description from the array
IFS='|' read -r GENOME_NAME GENOME_DESC <<< "$entry"
export GENOME_NAME GENOME_DESC
info "Processing: ${GENOME_NAME}..."
# 1. Remote Provisioning (Idempotent: skips if exists)
provider_create_repo "${GENOME_NAME}" "${GENOME_DESC}" "true"
GENOME_PATH="${WORK_DIR}/${MASTER_REPO}/${GENOME_NAME}"
if [ ! -d "${GENOME_PATH}" ]; then
info "Creating local directory and initializing scaffold..."
mkdir -p "${GENOME_PATH}"
cd "${GENOME_PATH}"
git init
# IMPORTANT: Initialize git-crypt BEFORE creating sensitive files
gcrypt_init
# Create directory structure and apply templates
scaffold_genome "."
install_precommit_hook "."
# Initial commit and push to remote
git add .
git commit -m "feat: initial scaffold for ${GENOME_NAME}"
SSH_URL=$(provider_ssh_url "${GENOME_NAME}")
git remote add origin "${SSH_URL}"
git push -u origin main
# Export the AES key for the user to back up
gcrypt_export_key "${GENOME_NAME}"
# 2. Link as submodule in the Master repository
cd "${WORK_DIR}/${MASTER_REPO}"
info "Linking ${GENOME_NAME} as a submodule..."
git submodule add "${SSH_URL}" "${GENOME_NAME}"
git add .gitmodules "${GENOME_NAME}"
git commit -m "feat: link submodule ${GENOME_NAME}"
else
warn "Genome directory '${GENOME_NAME}' already exists. Skipping local setup."
fi
done

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#!/usr/bin/env bash
# =============================================================================
# scripts/setup-master.sh
# Initializes the umbrella (Master) repository and core configurations.
# =============================================================================
set -euo pipefail
source "lib/output.sh"
source "config.env"
source "lib/scaffold.sh"
step "Configuring Master Repository: ${MASTER_REPO}"
# Ensure workspace exists
mkdir -p "${WORK_DIR}/${MASTER_REPO}"
cd "${WORK_DIR}/${MASTER_REPO}"
if [ ! -d ".git" ]; then
info "Initializing Git in Master repository..."
git init
# Optional: Add Karpathy's core reference as a read-only submodule
if [ -n "${GIST_URL:-}" ]; then
info "Adding core-karpathy as an external reference..."
git submodule add "${GIST_URL}" core-karpathy || warn "Could not add core-karpathy submodule."
fi
fi
# Apply master-level templates (README, AGENTS)
scaffold_master "."
# Initial commit for the master structure
git add .
git commit -m "chore: initialize master scaffold" || info "No changes to commit in master."

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#!/usr/bin/env bash
# =============================================================================
# scripts/setup.sh
# Main entry point for the Knowledge Genome framework initialization.
# Orchestrates dependency checks, master repo setup, and genome provisioning.
# =============================================================================
set -euo pipefail
# Resolve script directory and source core components
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
source "${SCRIPT_DIR}/lib/output.sh"
source "${SCRIPT_DIR}/config.env"
source "${SCRIPT_DIR}/lib/deps.sh"
step "Starting Knowledge Genome Setup"
# 1. Environment and Dependency Validation
info "Validating system dependencies..."
check_deps
check_git_identity
# 2. Master Repository Provisioning
info "Initializing Master Repository..."
bash "${SCRIPT_DIR}/scripts/setup-master.sh"
# 3. Genomes Provisioning (as defined in config.env)
info "Provisioning registered Genomes..."
bash "${SCRIPT_DIR}/scripts/setup-genomes.sh"
success "Setup process completed successfully!"
box "Next Steps:" \
"1. Navigate to master: cd ${WORK_DIR}/${MASTER_REPO}" \
"2. Secure your keys: Upload contents of ${KEYS_DIR} to Vaultwarden" \
"3. Start building: Add files to raw/articles/ and run your agents"

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# SYSTEM DIRECTIVE: Agent Schema `{{GENOME_NAME}}`
**[ROLE]**
You are the specialized AI maintainer for the `{{GENOME_NAME}}` genome. Read this schema before executing any file operations.
## 1. Genome Identity
- **Name:** `{{GENOME_NAME}}`
- **Domain Scope:** `{{GENOME_DESC}}`
- **Owner:** `{{FORGEJO_USER}}`
## 2. Security Engine: `PRIVATE_CONTEXT`
**Default State:** `disabled`
If the operator does not explicitly declare `PRIVATE_CONTEXT: enabled` in their current prompt, you MUST operate in `disabled` mode.
### Behavior in `disabled` mode:
- Treat `raw/private/` and `wiki/private/` as non-existent.
- Do not execute `cat`, `ls`, or `grep` on private paths.
- Refuse operator requests to summarize personal data.
### Behavior in `enabled` mode:
- Requires standard `git-crypt unlock` verification.
- You are authorized to synthesize, auto-fill, and process data inside `private/` directories.
- Outputs must be confined to `wiki/private/`. DO NOT leak private synthesis into public `wiki/concepts/`.
## 3. Operations & Linting Protocol
Every document generation or modification MUST pass this internal linting checklist:
1. **Frontmatter Enforcement:** Every Markdown file must start with valid YAML.
```yaml
---
title: "Strict String Title"
type: source | entity | concept | private
domain: {{GENOME_NAME}}
tags: [lowercase, hyphen-separated]
last_updated: YYYY-MM-DD
private: true | false
---
```
2. **Atomic Linking:** If you create `wiki/concepts/new-idea.md`, you MUST instantly add:
```text
* [[concepts/new-idea]] - <Brief summary>
```
to `wiki/index.md` under the appropriate heading, sorted alphabetically.
3. **Bi-directional Integrity:** Use Obsidian-style links `[[folder/file]]`. Do not use standard Markdown links `[text](url)` for internal references.
4. **Log the Action:** Append exactly ONE line to `wiki/log.md` detailing the operation.

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# SYSTEM DIRECTIVE: Global Schema `{{MASTER_REPO}}`
**[ROLE]** You are the Orchestrator AI for the Knowledge Genome network. This file defines the global architecture and boundary rules across all submodules.
## 1. Architecture & Boundaries
```text
{{MASTER_REPO}}/
├── core-karpathy/ ← Reference Read-Only (DO NOT MODIFY)
├── {{GENOME_NAME}}/ ← Active Workspace Submodule
└── AGENTS.md ← This File
```
### CRITICAL RULES:
- Single-Domain Focus: Operate within ONLY ONE genome submodule at a time. Do not attempt atomic commits across multiple genomes.
- Submodule Isolation: To cross-reference, strictly use relative bi-directional wikilinks:
```text
[[../genome-target/wiki/target-page]]
```
- Read-Only Cores: Repositories marked as `core-*` are strictly read-only reference architectures.
## 2. Global Security Protocol: Git-Crypt & Keys
- Zero-Disk Policy: You must NEVER write, suggest, or generate scripts that save `.key` files to the disk.
- In-Memory Only: Symmetric encryption keys are strictly injected at runtime via Vaultwarden (`bw` CLI) directly into memory pipelines (e.g., `<(bw get notes ...)`).
- Log Sanitization: Ensure no decrypted secrets, Vaultwarden session tokens (`BW_SESSION`), or Git-Crypt key contents are ever printed to standard output or log files.
## 3. Submodule Initialization State
To synchronize the workspace, the operational command is strictly:
```bash
git submodule update --init --recursive
```

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# --- Encryption Rules for Genomes ---
# These directories are stored as encrypted AES-256 blobs on the remote server.
# They require git-crypt and the specific genome key to be readable.
raw/private/** filter=git-crypt diff=git-crypt
wiki/private/** filter=git-crypt diff=git-crypt
# --- Binary Integrity ---
# Prevent line-ending conversion for encrypted files to avoid corruption.
raw/private/** -text
wiki/private/** -text
# --- Standard Text Configuration ---
*.md text eol=lf
*.sh text eol=lf
*.env text eol=lf
Makefile text eol=lf

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# --- Security Keys ---
# NEVER commit .key files to the repository
*.key
.resource_key
# --- Operating System Files ---
.DS_Store
Thumbs.db
.directory
*.swp
# --- Obsidian & Editor Configs ---
.obsidian/
.vscode/
.idea/
# --- Temporary Files & Local Logs ---
*.log
.tmp/
node_modules/

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#!/usr/bin/env bash
# =============================================================================
# .git/hooks/pre-commit
# Fail-safe security hook: Prevents plaintext leaks of sensitive data.
# =============================================================================
set -euo pipefail
# Directories that MUST be encrypted
PRIVATE_PATTERNS=("raw/private/" "wiki/private/")
FAILED=0
# Get staged files (excluding deletions)
STAGED_FILES=$(git diff --cached --name-only --diff-filter=ACM 2>/dev/null || true)
if [[ -z "$STAGED_FILES" ]]; then
exit 0
fi
for pattern in "${PRIVATE_PATTERNS[@]}"; do
while IFS= read -r file; do
if [[ "$file" == ${pattern}* ]]; then
# Check encryption status via git-crypt
STATUS=$(git-crypt status "$file" 2>/dev/null || echo "error")
if echo "$STATUS" | grep -q "not encrypted"; then
echo -e "\n\033[0;31m[SECURITY ALERT] PLAINTEXT LEAK DETECTED\033[0m"
echo "-----------------------------------------------------------"
echo "File: $file"
echo "Status: This file is in a private/ folder but is NOT encrypted."
echo "Action: Fix your .gitattributes or run 'git-crypt init'."
echo "-----------------------------------------------------------"
FAILED=1
fi
fi
done <<< "$STAGED_FILES"
done
if [[ "$FAILED" -ne 0 ]]; then
echo -e "\033[0;31mCommit blocked for security reasons.\033[0m\n"
exit 1
fi
exit 0

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---
title: "Index — {{GENOME_NAME}}"
type: index
domain: {{GENOME_NAME}}
last_updated: {{DATE}}
private: false
---
# Master Index: {{GENOME_NAME}}
**[AGENT INSTRUCTION]**
Maintain strict alphabetical sorting within each section. Ensure the `last_updated` YAML field is modified upon every edit. Use only `[[slug]] - Summary` format.
---
## Sources (`wiki/sources/`)
*Ingested raw materials.*
## Entities (`wiki/entities/`)
*People, organizations, tools.*
## Concepts (`wiki/concepts/`)
*Theories, methodologies, architecture.*
## Private Synthesis (`wiki/private/`)
*Restricted access. Use slug names ONLY. Do not append summaries to prevent metadata leakage.*

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---
title: "Operations Log — {{GENOME_NAME}}"
type: log
domain: {{GENOME_NAME}}
private: false
---
# Operations Log: {{GENOME_NAME}}
**[AGENT INSTRUCTION]**
This is an append-only system ledger. Do not edit previous lines.
Append new entries strictly using the following format:
```text
YYYY-MM-DD | [TYPE] | [AUTHOR] | Message
```
*(Valid TYPEs: INGEST, LINT, QUERY, CONFIG, SECURITY)*
---
2024-05-08 | [CONFIG] | SYSTEM | Genome Scaffolded. Directory structure and encryption layer initialized.