From b23efea14e319a67a7cc75f14df5f41a3b65119c Mon Sep 17 00:00:00 2001
From: Matteo Cherubini <cherubinimatte@gmail.com>
Date: Fri, 8 May 2026 21:09:42 +0200
Subject: [PATCH] feat: Develop core scaffolding engine and Git configuration
 templates

---
 lib/scaffold.sh         | 67 +++++++++++++++++++++++++++++++++++++++++
 templates/gitattributes | 17 +++++++++++
 templates/gitignore     | 20 ++++++++++++
 3 files changed, 104 insertions(+)
 create mode 100644 lib/scaffold.sh
 create mode 100644 templates/gitattributes
 create mode 100644 templates/gitignore

diff --git a/lib/scaffold.sh b/lib/scaffold.sh
new file mode 100644
index 0000000..0bea0bd
--- /dev/null
+++ b/lib/scaffold.sh
@@ -0,0 +1,67 @@
+#!/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."
+}
diff --git a/templates/gitattributes b/templates/gitattributes
new file mode 100644
index 0000000..226c36e
--- /dev/null
+++ b/templates/gitattributes
@@ -0,0 +1,17 @@
+# --- 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
diff --git a/templates/gitignore b/templates/gitignore
new file mode 100644
index 0000000..6605615
--- /dev/null
+++ b/templates/gitignore
@@ -0,0 +1,20 @@
+# --- 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/