docs: Add AI agent instructions for wiki files

templates/gitattributes

@@ -1,17 +1,14 @@
-# --- 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
+
+# --- Encryption Rules ---
+# MUST come after text rules: in .gitattributes the last matching rule wins per attribute.
+# Placing **/private/** here ensures -text overrides the *.md text=lf rule above,
+# preventing EOL conversion from corrupting AES-256 encrypted blobs.
+#
+# **/private/** catches any private/ directory at any depth in the repo,
+# including directories created at runtime by the LLM agent.
+**/private/**   filter=git-crypt diff=git-crypt -text

templates/pre-commit.sh

@@ -1,49 +1,47 @@
 #!/usr/bin/env bash
 # =============================================================================
 # .git/hooks/pre-commit
-# Fail-safe security hook: Prevents plaintext leaks of sensitive data.
+# Fail-safe security hook: prevents plaintext commits of encrypted files.
+# Reads encryption requirements dynamically from .gitattributes via
+# git check-attr — no hardcoded paths, inherits all future rules automatically.
 # =============================================================================
 
 set -euo pipefail
 
-# Directories that MUST be encrypted
-PRIVATE_PATTERNS=("raw/private/" "wiki/private/")
 FAILED=0
 
-# Check on git-crypt
+# Verify git-crypt is initialized
 if [[ ! -d ".git-crypt" ]]; then
-  echo -e "\n\033[0;31m[CRITICAL] git-crypt is not initialized in this repository.\033[0m"
-  echo "Run 'git-crypt init' and 'make setup' before committing."
+    printf "\n\033[0;31m[CRITICAL] git-crypt not initialized.\033[0m\n"
+    printf "Run 'git-crypt init' and 'make setup' before committing.\n"
     exit 1
 fi
 
-# Get staged files (excluding deletions)
+# Get staged files (additions, copies, modifications — no deletions)
 STAGED_FILES=$(git diff --cached --name-only --diff-filter=ACM 2>/dev/null || true)
 
-if [[ -z "$STAGED_FILES" ]]; then
-  exit 0
-fi
+[[ -z "$STAGED_FILES" ]] && exit 0
 
-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:   $file"
-        echo "Status: This file is in a private/ folder but is NOT encrypted."
-        echo "Action: Fix your .gitattributes or run 'git-crypt init'."
-        echo "-----------------------------------------------------------"
+    # Dynamically check if this file requires git-crypt encryption
+    filter=$(git check-attr filter -- "$file" 2>/dev/null | sed 's/.*: //')
+    [[ "$filter" != "git-crypt" ]] && continue
+
+    # File is required to be encrypted — verify it actually is
+    status=$(git-crypt status "$file" 2>/dev/null || printf "error")
+    if printf '%s\n' "$status" | grep -q "not encrypted"; then
+        printf "\n\033[0;31m[SECURITY ALERT] PLAINTEXT LEAK DETECTED\033[0m\n"
+        printf -- "-----------------------------------------------------------\n"
+        printf "File:   %s\n" "$file"
+        printf "Status: Marked for git-crypt in .gitattributes but NOT encrypted.\n"
+        printf "Action: Verify .gitattributes rules and re-run 'git-crypt init'.\n"
+        printf -- "-----------------------------------------------------------\n"
         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"
+    printf "\n\033[0;31mCommit blocked: security policy violation.\033[0m\n\n"
     exit 1
 fi
 

templates/wiki-index.md

@@ -11,7 +11,8 @@ private: false
 
 **[AGENT INSTRUCTION]**
 This is the primary navigation file. Read it first on every session before accessing individual pages.
-Maintain strict alphabetical sorting within each section.
+Append new entries at the bottom of the relevant section — do not reorder or rewrite sections.
+Alphabetical sorting is handled automatically by the pre-commit hook.
 Update `last_updated` in the YAML frontmatter on every edit.
 Entry format: `- [[folder/slug]] — One-line summary. \`maturity: <value>\``
 

templates/wiki-log.md

@@ -9,6 +9,10 @@ private: false
 
 # Operations Log: {{GENOME_NAME}}
 
+**[ORCHESTRATOR]**
+Inject only the last 20 entries into agent context: `tail -n 20 wiki/log.md`
+The agent must never load or read the full log file — it grows unbounded.
+
 **[AGENT INSTRUCTION]**
 This is an append-only system ledger. Never edit or delete previous entries.
 Append new entries at the bottom using the format defined below.