From c889fe1ceaff4a24c2ad2f490ca708e2a61cb26e Mon Sep 17 00:00:00 2001
From: Amr Gharbeia <amr@gharbeia.net>
Date: Fri, 17 Apr 2026 17:38:37 -0400
Subject: [PATCH] fix(setup): Make SCRIPT_DIR symlink-aware and harden
 bootstrapper logic

---
 literate/setup.org | 12 ++++++++++--
 opencortex.sh      | 12 ++++++++++--
 2 files changed, 20 insertions(+), 4 deletions(-)

diff --git a/literate/setup.org b/literate/setup.org
index bf58069..d311213 100644
--- a/literate/setup.org
+++ b/literate/setup.org
@@ -15,10 +15,18 @@ HOST=${1:-localhost}
 RED='\033[0;31m'; GREEN='\033[0;32m'; BLUE='\033[0;34m'; YELLOW='\033[0;33m'; NC='\033[0m'
 
 command_exists() { command -v "$1" >/dev/null 2>&1; }
-SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
+# Resolve symlinks to find the actual repository location
+SOURCE="${BASH_SOURCE[0]}"
+while [ -h "$SOURCE" ]; do
+    DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+    SOURCE="$(readlink "$SOURCE")"
+    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
+done
+SCRIPT_DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
 
 # --- 1. BOOTSTRAP ---
-if [ ! -d "$SCRIPT_DIR/.git" ] && [[ ! "$(pwd)" =~ "opencortex" ]]; then
+# Only bootstrap if we are not in a git repo and the target hidden folder does not exist
+if [ ! -d "$SCRIPT_DIR/.git" ] && [ ! -d "$HOME/.opencortex" ] && [[ ! "$(pwd)" =~ "opencortex" ]]; then
     echo -e "${BLUE}=== OpenCortex: Zero-to-One Bootstrapper ===${NC}"
     git clone http://10.10.10.201:3001/amr/opencortex.git ~/.opencortex
     cd ~/.opencortex && git submodule update --init --recursive
diff --git a/opencortex.sh b/opencortex.sh
index 105ce49..17e343a 100755
--- a/opencortex.sh
+++ b/opencortex.sh
@@ -6,10 +6,18 @@ HOST=${1:-localhost}
 RED='\033[0;31m'; GREEN='\033[0;32m'; BLUE='\033[0;34m'; YELLOW='\033[0;33m'; NC='\033[0m'
 
 command_exists() { command -v "$1" >/dev/null 2>&1; }
-SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
+# Resolve symlinks to find the actual repository location
+SOURCE="${BASH_SOURCE[0]}"
+while [ -h "$SOURCE" ]; do
+    DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+    SOURCE="$(readlink "$SOURCE")"
+    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
+done
+SCRIPT_DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
 
 # --- 1. BOOTSTRAP ---
-if [ ! -d "$SCRIPT_DIR/.git" ] && [[ ! "$(pwd)" =~ "opencortex" ]]; then
+# Only bootstrap if we are not in a git repo and the target hidden folder does not exist
+if [ ! -d "$SCRIPT_DIR/.git" ] && [ ! -d "$HOME/.opencortex" ] && [[ ! "$(pwd)" =~ "opencortex" ]]; then
     echo -e "${BLUE}=== OpenCortex: Zero-to-One Bootstrapper ===${NC}"
     git clone http://10.10.10.201:3001/amr/opencortex.git ~/.opencortex
     cd ~/.opencortex && git submodule update --init --recursive