Proactive doctor, setup wizard, and TUI fixes

BREAKING CHANGES / KNOWN ISSUES:
- 8 skills have syntax errors causing loader warnings:
  org-skill-bouncer, org-skill-config-manager, org-skill-credentials-vault,
  org-skill-engineering-standards, org-skill-gardener, org-skill-homoiconic-memory,
  org-skill-peripheral-vision, org-skill-policy
- These skills fail to load but don't block system operation
- TUI works despite these errors

FEATURES ADDED:

1. Proactive Doctor System
   - Doctor runs automatically on daemon startup
   - Health check runs before accepting connections
   - Adds /health endpoint for health status queries
   - *system-health* variable tracks: :healthy, :degraded, :unhealthy, :unknown

2. Error Handling (Option B - Debugger Hook)
   - TUI and CLI now run doctor diagnostics on errors
   - Shows "Run opencortex doctor" message on crash
   - Suggests repair commands after failures

3. Interactive Setup Wizard (org-skill-config-manager)
   - Full wizard implemented in config-manager skill:
     * LLM provider configuration (OpenAI, Anthropic, OpenRouter, Groq, Gemini, Ollama)
     * Gateway linking (Slack, Discord)
     * Memory settings (auto-save interval, history retention)
     * Network settings (timeout, proxy)
   - Saves to ~/.config/opencortex/.env (KEY=VALUE format)
   - CLI integration: opencortex setup, setup --add-provider, setup --link

4. CLI Enhancements
   - doctor --watch: Background health monitoring (60s interval)
   - doctor --fix: Interactive repair (falls back to full setup if core files missing)
   - setup command runs wizard or delegates to setup_system

5. TUI Fixes
   - Inlined message formatting to avoid dependency issues
   - Added error handling in handle-return
   - Cleaner error messages

6. Thin Harness Compliance
   - Removed doctor from harness (now in org-skill-diagnostics skill)
   - XDG directories: only .lisp in harness, .org kept in skills for loader

harness/communication.org

@@ -83,6 +83,17 @@ The ~communication.lisp~ module defines the low-level transport and framing logi
               (cond
                 ((eq msg :eof) (return))
                 ((eq msg :error) (return))
+                ((eq (getf msg :type) :health-check)
+                 ;; Handle health check request
+                 (let ((health-msg (list :type :health-response 
+                                          :status (or (and (boundp 'opencortex::*system-health*) 
+                                                          (symbol-value 'opencortex::*system-health*))
+                                                      :unknown)
+                                          :checked-p (or (and (boundp 'opencortex::*health-check-ran*)
+                                                              (symbol-value 'opencortex::*health-check-ran*))
+                                                      nil))))
+                   (format stream "~a" (frame-message health-msg))
+                   (finish-output stream)))
                 (t (inject-stimulus msg :stream stream))))))
       (error (c) (harness-log "CLIENT ERROR: ~a" c)))
     (ignore-errors (usocket:socket-close socket))))

harness/loop.org

@@ -96,6 +96,44 @@ The Metabolic Loop is the fundamental rhythm of OpenCortex: the continuous proce
 (defvar *shutdown-save-enabled* t)
 #+end_src
 
+** Health Status
+#+begin_src lisp
+(defvar *system-health* :unknown
+  "Current system health status: :healthy, :degraded, :unhealthy, or :unknown.")
+
+(defvar *health-check-ran* nil
+  "Flag indicating if initial health check has completed.")
+#+end_src
+
+** Proactive Doctor
+#+begin_src lisp
+(defun run-startup-health-check ()
+  "Runs the doctor diagnostics on startup. Returns health status."
+  (format t "~%")
+  (format t "==================================================~%")
+  (format t " DOCTOR: Running Startup Health Check~%")
+  (format t "==================================================~%")
+  (handler-case
+      (progn
+        (when (fboundp 'doctor-run-all)
+          (let ((result (doctor-run-all :auto-install nil)))
+            (setf *health-check-ran* t)
+            (if result
+                (progn
+                  (setf *system-health* :healthy)
+                  (format t "DAEMON: Health check passed. Starting services.~%"))
+                (progn
+                  (setf *system-health* :degraded)
+                  (format t "DAEMON: Health check found issues.~%")
+                  (format t "         Run 'opencortex doctor --fix' to repair.~%")))))
+        (setf *health-check-ran* t))
+    (error (c)
+      (format t "DOCTOR ERROR: ~a~%" c)
+      (setf *system-health* :unhealthy)
+      (setf *health-check-ran* t)))
+  (format t "==================================================~%~%"))
+#+end_src
+
 ** Main Entry Point (main)
 #+begin_src lisp
 (defun main ()
@@ -108,16 +146,20 @@ The Metabolic Loop is the fundamental rhythm of OpenCortex: the continuous proce
   (load-memory-from-disk)
   (initialize-actuators)
   (initialize-all-skills)
+  
+  ;; Run proactive doctor before starting services
+  (run-startup-health-check)
+  
   (start-heartbeat)
   (start-daemon)
 
   #+sbcl
   (sb-sys:enable-interrupt sb-unix:sigint
-                           (lambda (sig code scp)
-                             (declare (ignore sig code scp))
-                             (harness-log "SHUTDOWN: SIGINT received. Saving memory...")
-                             (when *shutdown-save-enabled* (save-memory-to-disk))
-                             (uiop:quit 0)))
+                            (lambda (sig code scp)
+                              (declare (ignore sig code scp))
+                              (harness-log "SHUTDOWN: SIGINT received. Saving memory...")
+                              (when *shutdown-save-enabled* (save-memory-to-disk))
+                              (uiop:quit 0)))
 
   (let ((sleep-interval (or (ignore-errors (parse-integer (uiop:getenv "DAEMON_SLEEP_INTERVAL"))) 3600)))
     (loop

harness/tui-client.org

@@ -38,7 +38,7 @@ The OpenCortex TUI Client is a standalone Common Lisp application built on **Cro
 #+begin_src lisp
 (in-package :cl-user)
 (defpackage :opencortex.tui
-  (:use :cl :croatoan)
+  (:use :cl :croatoan :usocket)
   (:export :main))
 (in-package :opencortex.tui)
 #+end_src
@@ -108,13 +108,18 @@ The OpenCortex TUI Client is a standalone Common Lisp application built on **Cro
     (when (> (length cmd) 0)
       (enqueue-msg (format nil "⬆ ~a" cmd))
       (handler-case
-          (when (and stream (open-stream-p stream))
-            (format stream "~a" (opencortex:frame-message (list :TYPE :EVENT 
-                                                               :META (list :SOURCE :tui)
-                                                               :PAYLOAD (list :SENSOR :user-input :TEXT cmd))))
-            (finish-output stream))
+          (progn
+            (when (and stream (open-stream-p stream))
+              (let* ((msg (list :TYPE :EVENT 
+                               :META (list :SOURCE :tui)
+                               :PAYLOAD (list :SENSOR :user-input :TEXT cmd)))
+                     (payload (format nil "~s" msg))
+                     (len (length payload)))
+                (format stream "~6,'0x~a" len payload)
+                (finish-output stream)))
+            (enqueue-msg "✓ Sent"))
         (error (c)
-          (declare (ignore c))
+          (format t "Send error: ~a~%" c)
           (enqueue-msg "ERROR: Connection to daemon lost.")
           (setf *is-running* nil))))
     (when (string= cmd "/exit") (setf *is-running* nil))

opencortex.sh

@@ -32,6 +32,32 @@ if [ -f "$OC_CONFIG_DIR/.env" ]; then
     source "$OC_CONFIG_DIR/.env"
 fi
 
+# --- Dependency Checker ---
+check_dependencies() {
+    local missing=()
+    for dep in sbcl emacs git curl socat nc; do
+        if ! command_exists "$dep"; then
+            missing+=("$dep")
+        fi
+    done
+    
+    if [ ${#missing[@]} -gt 0 ]; then
+        echo -e "${YELLOW}--- Missing dependencies: ${missing[*]} ---${NC}"
+        if command_exists apt-get; then
+            echo "Attempting to install missing dependencies..."
+            if sudo apt-get update && sudo apt-get install -y sbcl emacs-nox rlwrap netcat-openbsd curl git socat libssl-dev libncurses-dev libffi-dev zlib1g-dev libsqlite3-dev 2>/dev/null; then
+                echo -e "${GREEN}✓ Dependencies installed successfully${NC}"
+            else
+                echo -e "${RED}✗ Could not install dependencies. Please run with sudo or install manually:${NC}"
+                echo "  sudo apt-get install sbcl emacs-nox rlwrap netcat-openbsd curl git socat"
+            fi
+        else
+            echo -e "${RED}✗ Cannot auto-install: apt-get not available${NC}"
+            echo "Please install manually: sbcl emacs git curl socat netcat-openbsd"
+        fi
+    fi
+}
+
 # --- 2. SETUP ---
 setup_system() {
     NON_INTERACTIVE=false
@@ -60,25 +86,32 @@ setup_system() {
     cp "$SCRIPT_DIR/opencortex.asd" "$OC_DATA_DIR/"
     cp "$SCRIPT_DIR/harness"/*.org "$OC_DATA_DIR/harness/"
     cp "$SCRIPT_DIR/skills"/*.org "$OC_DATA_DIR/skills/"
+    
+    # Create tests directory before tangling (some org files write to tests/)
+    mkdir -p "$OC_DATA_DIR/tests"
 
     export INSTALL_DIR="$OC_DATA_DIR"
 
     # Critical: Tangle manifest first to establish system structure (into root)
     echo "Tangling harness/manifest.org..."
-    (cd "$OC_DATA_DIR" && emacs -Q --batch --eval "(require 'org)" --eval "(setq org-confirm-babel-evaluate nil)" --eval "(org-babel-tangle-file \"$OC_DATA_DIR/harness/manifest.org\")" >/dev/null 2>&1) || true
+    (cd "$OC_DATA_DIR" && emacs -Q --batch --eval "(require 'org)" --eval "(setq org-confirm-babel-evaluate nil)" --eval "(org-babel-tangle-file \"harness/manifest.org\")") >/dev/null 2>&1 || true
 
     # Tangle harness files into harness/
-    for f in harness/*.org; do
-        if [ "$f" != "harness/manifest.org" ]; then
-            echo "Tangling $f..."
-            (cd "$OC_DATA_DIR/harness" && emacs -Q --batch --eval "(require 'org)" --eval "(setq org-confirm-babel-evaluate nil)" --eval "(org-babel-tangle-file \"$OC_DATA_DIR/$f\")" >/dev/null 2>&1) || true
+    for f in "$SCRIPT_DIR/harness"/*.org; do
+        fname=$(basename "$f" .org)
+        if [ "$fname" != "manifest" ]; then
+            echo "Tangling harness/$fname.org..."
+            (cd "$OC_DATA_DIR/harness" && emacs -Q --batch --eval "(require 'org)" --eval "(setq org-confirm-babel-evaluate nil)" --eval "(org-babel-tangle-file \"${fname}.org\")") >/dev/null 2>&1 || true
         fi
     done
 
     # Tangle skill files into skills/
-    for f in skills/*.org; do
-        echo "Tangling $f..."
-        (cd "$OC_DATA_DIR/skills" && emacs -Q --batch --eval "(require 'org)" --eval "(setq org-confirm-babel-evaluate nil)" --eval "(org-babel-tangle-file \"$OC_DATA_DIR/$f\")" >/dev/null 2>&1) || true
+    for f in "$SCRIPT_DIR/skills"/*.org; do
+        fname=$(basename "$f" .org)
+        echo "Tangling skills/$fname.org..."
+        # Copy org to XDG first (skills need to be loaded from XDG path)
+        cp "$f" "$OC_DATA_DIR/skills/"
+        (cd "$OC_DATA_DIR/skills" && emacs -Q --batch --eval "(require 'org)" --eval "(setq org-confirm-babel-evaluate nil)" --eval "(org-babel-tangle-file \"${fname}.org\")") >/dev/null 2>&1 || true
     done
 
     # Special handling for tests that need to go into tests/
@@ -88,6 +121,11 @@ setup_system() {
     
     # Also move run-all-tests.lisp if it landed in the wrong place
     [ -f "$OC_DATA_DIR/run-all-tests.lisp" ] && mv "$OC_DATA_DIR/run-all-tests.lisp" "$OC_DATA_DIR/harness/"
+
+    # Cleanup: Remove .org files from XDG harness only (skills need .org for loader)
+    echo "Cleaning up .org files from XDG harness..."
+    rm -f "$OC_DATA_DIR/harness"/*.org
+
     cd "$SCRIPT_DIR"    # Create the bin shim
     echo -e "${YELLOW}--- Creating Bin Shim in $OC_BIN_DIR/opencortex ---${NC}"
     ln -sf "$SCRIPT_DIR/opencortex.sh" "$OC_BIN_DIR/opencortex"
@@ -107,6 +145,66 @@ setup_system() {
          --eval '(funcall (find-symbol "RUN-SETUP-WIZARD" :opencortex))'
 }
 
+# --- Doctor Repair (Lightweight Fix) ---
+doctor_repair() {
+    echo -e "${BLUE}=== OpenCortex: Repair Mode ===${NC}"
+    
+    # 1. Fix system dependencies
+    echo -e "${YELLOW}--- Fixing System Dependencies ---${NC}"
+    check_dependencies
+    
+    # 2. Ensure XDG directories exist
+    echo -e "${YELLOW}--- Fixing XDG Directories ---${NC}"
+    mkdir -p "$OC_CONFIG_DIR" "$OC_DATA_DIR" "$OC_STATE_DIR" "$OC_BIN_DIR"
+    mkdir -p "$OC_DATA_DIR/harness" "$OC_DATA_DIR/tests" "$OC_DATA_DIR/skills" "$OC_DATA_DIR/library"
+    
+    # 3. Re-tangle harness files that may be broken
+    echo -e "${YELLOW}--- Re-tangling Harness Files ---${NC}"
+    for f in "$SCRIPT_DIR/harness"/*.org; do
+        if [ -f "$f" ]; then
+            fname=$(basename "$f" .org)
+            echo "  Checking harness/$fname..."
+            # Try to load each harness file - if it fails, re-tangle
+            if ! sbcl --non-interactive \
+                 --eval "(load \"$OC_DATA_DIR/harness/${fname}.lisp\")" \
+                 --eval "(format t \"OK~%\")" 2>/dev/null | grep -q "OK"; then
+                echo "    Re-tangling $fname.org..."
+                (cd "$OC_DATA_DIR/harness" && emacs -Q --batch \
+                    --eval "(require 'org)" \
+                    --eval "(setq org-confirm-babel-evaluate nil)" \
+                    --eval "(org-babel-tangle-file \"$f\")" >/dev/null 2>&1) || true
+            fi
+        fi
+    done
+    
+    # 4. Re-tangle skill files that may be broken
+    echo -e "${YELLOW}--- Re-tangling Skill Files ---${NC}"
+    for f in "$SCRIPT_DIR/skills"/*.org; do
+        if [ -f "$f" ]; then
+            fname=$(basename "$f" .org)
+            echo "  Checking skill/$fname..."
+            # Copy .org to XDG temporarily for tangle, then remove
+            cp "$f" "$OC_DATA_DIR/skills/"
+            if ! sbcl --non-interactive \
+                 --eval "(load \"$OC_DATA_DIR/skills/${fname}.lisp\")" \
+                 --eval "(format t \"OK~%\")" 2>/dev/null | grep -q "OK"; then
+                echo "    Re-tangling $fname.org..."
+                (cd "$OC_DATA_DIR/skills" && emacs -Q --batch \
+                    --eval "(require 'org)" \
+                    --eval "(setq org-confirm-babel-evaluate nil)" \
+                    --eval "(org-babel-tangle-file \"$OC_DATA_DIR/skills/${fname}.org\")" >/dev/null 2>&1) || true
+            fi
+            rm -f "$OC_DATA_DIR/skills/${fname}.org"
+        fi
+    done
+    
+    # 5. Cleanup .org files
+    rm -f "$OC_DATA_DIR/harness"/*.org "$OC_DATA_DIR/skills"/*.org 2>/dev/null || true
+    
+    echo -e "${GREEN}--- Repair Complete ---${NC}"
+    echo "Run 'opencortex doctor' to verify the system."
+}
+
 # --- 3. COMMAND ROUTER ---
 COMMAND=$1
 [ -z "$COMMAND" ] && COMMAND="cli"
@@ -116,23 +214,82 @@ case "$COMMAND" in
     link)
         PLATFORM=$1
         TOKEN=$2
+        check_dependencies
         exec sbcl --non-interactive              --eval '(load (merge-pathnames "quicklisp/setup.lisp" (user-homedir-pathname)))'              --eval "(push (truename \"$OC_DATA_DIR/\") asdf:*central-registry*)"              --eval '(ql:quickload :opencortex)'              --eval '(opencortex:initialize-all-skills)'              --eval "(funcall (find-symbol \"GATEWAY-MANAGER-MAIN\" :opencortex) \"$PLATFORM\" \"$TOKEN\")"
         ;;
 
     doctor)
-        exec sbcl --non-interactive \
-             --eval '(load (merge-pathnames "quicklisp/setup.lisp" (user-homedir-pathname)))' \
-             --eval "(push (truename \"$OC_DATA_DIR/\") asdf:*central-registry*)" \
-             --eval '(ql:quickload :opencortex)' \
-             --eval '(opencortex:initialize-all-skills)' \
-             --eval '(funcall (find-symbol "DOCTOR-MAIN" :opencortex))'
+        check_dependencies
+        if [ "$1" = "--watch" ]; then
+            echo "Starting background health monitor (60s interval)..."
+            echo "Press Ctrl+C to stop."
+            echo ""
+            while true; do
+                echo "--- $(date '+%Y-%m-%d %H:%M:%S') ---"
+                sbcl --non-interactive \
+                     --eval '(load (merge-pathnames "quicklisp/setup.lisp" (user-homedir-pathname)))' \
+                     --eval "(push (truename \"$OC_DATA_DIR/\") asdf:*central-registry*)" \
+                     --eval '(ql:quickload :opencortex)' \
+                     --eval '(opencortex:initialize-all-skills)' \
+                     --eval '(funcall (find-symbol "DOCTOR-RUN-ALL" :opencortex))' \
+                     --eval '(uiop:quit 0)' 2>&1 | grep -E "(HEALTH|OK|FAIL|WARN|SYSTEM|===)" || true
+                sleep 60
+            done
+        elif [ "$1" = "--fix" ]; then
+            # Check if major harness files exist - if not, run full setup
+            if [ ! -f "$OC_DATA_DIR/harness/package.lisp" ] || [ ! -f "$OC_DATA_DIR/harness/skills.lisp" ]; then
+                echo "Core files missing. Running full setup..."
+                setup_system "$@"
+            else
+                echo "Repairing system..."
+                doctor_repair
+            fi
+        else
+            exec sbcl --non-interactive \
+                 --eval '(load (merge-pathnames "quicklisp/setup.lisp" (user-homedir-pathname)))' \
+                 --eval "(push (truename \"$OC_DATA_DIR/\") asdf:*central-registry*)" \
+                 --eval '(ql:quickload :opencortex)' \
+                 --eval '(opencortex:initialize-all-skills)' \
+                 --eval '(funcall (find-symbol "DOCTOR-MAIN" :opencortex))'
+        fi
         ;;
 
     setup)
-        setup_system "$@"
+        check_dependencies
+        if [ "$1" = "--add-provider" ]; then
+            echo "Adding LLM provider..."
+            sbcl --non-interactive \
+                 --eval '(load (merge-pathnames "quicklisp/setup.lisp" (user-homedir-pathname)))' \
+                 --eval "(push (truename \"$OC_DATA_DIR/\") asdf:*central-registry*)" \
+                 --eval '(ql:quickload :opencortex)' \
+                 --eval '(opencortex:initialize-all-skills)' \
+                 --eval '(funcall (find-symbol "SETUP-ADD-PROVIDER" :opencortex))'
+        elif [ "$1" = "--link" ]; then
+            PLATFORM=$2
+            TOKEN=$3
+            if [ -z "$PLATFORM" ] || [ -z "$TOKEN" ]; then
+                echo "Usage: opencortex setup --link <platform> <token>"
+                echo "  platforms: slack, discord"
+                exit 1
+            fi
+            echo "Linking $PLATFORM gateway..."
+            $0 link "$PLATFORM" "$TOKEN"
+        elif [ "$1" = "--non-interactive" ]; then
+            setup_system "$@"
+        else
+            # Run interactive setup wizard
+            echo "Starting interactive setup wizard..."
+            sbcl --non-interactive \
+                 --eval '(load (merge-pathnames "quicklisp/setup.lisp" (user-homedir-pathname)))' \
+                 --eval "(push (truename \"$OC_DATA_DIR/\") asdf:*central-registry*)" \
+                 --eval '(ql:quickload :opencortex)' \
+                 --eval '(opencortex:initialize-all-skills)' \
+                 --eval '(funcall (find-symbol "RUN-SETUP-WIZARD" :opencortex))'
+        fi
         ;;
 
     boot|--boot)
+        check_dependencies
         exec sbcl --non-interactive \
              --eval '(load (merge-pathnames "quicklisp/setup.lisp" (user-homedir-pathname)))' \
              --eval "(push (truename \"$OC_DATA_DIR/\") asdf:*central-registry*)" \
@@ -140,16 +297,71 @@ case "$COMMAND" in
              --eval '(opencortex:main)'
         ;;
 
+    daemon)
+        check_dependencies
+        echo "Starting OpenCortex daemon in background..."
+        nohup sbcl --non-interactive \
+             --eval '(load (merge-pathnames "quicklisp/setup.lisp" (user-homedir-pathname)))' \
+             --eval "(push (truename \"$OC_DATA_DIR/\") asdf:*central-registry*)" \
+             --eval "(ql:quickload '(:opencortex :croatoan))" \
+             --eval '(opencortex:main)' \
+             > "$OC_STATE_DIR/daemon.log" 2>&1 &
+        echo "Daemon started. Waiting for port 9105..."
+        for i in {1..20}; do
+            if ss -tln | grep -q 9105; then
+                echo "✓ Daemon ready on port 9105"
+                exit 0
+            fi
+            sleep 1
+        done
+        echo "✗ Daemon failed to start. Check $OC_STATE_DIR/daemon.log"
+        exit 1
+        ;;
+
     tui)
-        exec sbcl \
+        check_dependencies
+        if ! ss -tln | grep -q 9105; then
+            echo "Daemon not running. Starting daemon first..."
+            $0 daemon
+        fi
+        if sbcl --non-interactive \
              --eval '(load (merge-pathnames "quicklisp/setup.lisp" (user-homedir-pathname)))' \
              --eval "(push (truename \"$OC_DATA_DIR/\") asdf:*central-registry*)" \
              --eval '(ql:quickload :opencortex/tui)' \
-             --eval '(opencortex.tui:main)'
+             --eval '(opencortex.tui:main)'; then
+            true
+        else
+            EXIT_CODE=$?
+            echo ""
+            echo "TUI exited with error. Running diagnostics..."
+            $0 doctor
+            echo ""
+            echo "Run 'opencortex doctor --fix' to repair, or 'opencortex setup' to reconfigure."
+            exit $EXIT_CODE
+        fi
+        ;;
+
+    cli|boot)
+        check_dependencies
+        if sbcl --non-interactive \
+             --eval '(load (merge-pathnames "quicklisp/setup.lisp" (user-homedir-pathname)))' \
+             --eval "(push (truename \"$OC_DATA_DIR/\") asdf:*central-registry*)" \
+             --eval "(ql:quickload '(:opencortex :croatoan))" \
+             --eval '(opencortex:main)'; then
+            true
+        else
+            EXIT_CODE=$?
+            echo ""
+            echo "CLI exited with error. Running diagnostics..."
+            $0 doctor
+            echo ""
+            echo "Run 'opencortex doctor --fix' to repair, or 'opencortex setup' to reconfigure."
+            exit $EXIT_CODE
+        fi
         ;;
 
     *)
-        echo "Available commands: setup, link, doctor, boot, tui"
+        echo "Available commands: setup, link, doctor, boot, tui, cli, daemon"
         exit 1
         ;;
 esac

skills/org-skill-bouncer.org

@@ -16,8 +16,8 @@ The *Bouncer Skill* is the physical security layer of OpenCortex. It enforces op
 ** Security Configuration
 #+begin_src lisp
 (defvar *bouncer-network-whitelist*
-  '("api.telegram.org" "matrix.org" "googleapis.com" "openai.com" "anthropic.com
-  "Domains that the Bouncer considers safe for outbound connections.
+  '("api.telegram.org" "matrix.org" "googleapis.com" "openai.com" "anthropic.com")
+  "Domains that the Bouncer considers safe for outbound connections.")
 #+end_src
 
 ** Secret Scanning (bouncer-scan-secrets)
@@ -56,9 +56,9 @@ The *Bouncer Skill* is the physical security layer of OpenCortex. It enforces op
   (let* ((target (proto-get action :target))
          (payload (proto-get action :payload))
          (text (or (proto-get payload :text) (proto-get action :text)))
-         (cmd (or (proto-get payload :cmd)
-                 (when (and (eq target :tool) (equal (proto-get payload :tool) "shell)
-                   (proto-get (proto-get payload :args) :cmd))))
+(cmd (or (proto-get payload :cmd)
+                  (when (and (eq target :tool) (equal (proto-get payload :tool) "shell"))
+                    (proto-get (proto-get payload :args) :cmd)))))
          (approved (proto-get action :approved)))
 
     (cond
@@ -71,15 +71,15 @@ The *Bouncer Skill* is the physical security layer of OpenCortex. It enforces op
                :payload (list :level :error
                               :text (format nil "Action blocked: Potential exposure of '~a'" secret-name)))))
 
-      ((and (or (eq target :shell)
-               (and (eq target :tool) (equal (proto-get payload :tool) "shell))
-            (bouncer-check-network-exfil cmd))
-       (harness-log "SECURITY WARNING: External network call detected. Queuing for approval.
+((and (or (eq target :shell)
+                (and (eq target :tool) (equal (proto-get payload :tool) "shell")))
+             (bouncer-check-network-exfil cmd))
+        (harness-log "SECURITY WARNING: External network call detected. Queuing for approval."))
        (list :type :EVENT :payload (list :sensor :approval-required :action action)))
 
-      ((or (member target '(:shell))
-          (and (eq target :tool) (member (proto-get payload :tool) '("shell" "repair-file :test #'string=))
-          (and (eq target :emacs) (eq (proto-get payload :action) :eval)))
+((or (member target '(:shell))
+           (and (eq target :tool) (member (proto-get payload :tool) '("shell" "repair-file") :test #'string=))
+           (and (eq target :emacs) (eq (proto-get payload :action) :eval))))
        (harness-log "SECURITY: High-impact action requires approval: ~a" (or (proto-get payload :tool) target))
        (list :type :EVENT :payload (list :sensor :approval-required :action action)))
 
@@ -90,7 +90,7 @@ The *Bouncer Skill* is the physical security layer of OpenCortex. It enforces op
 #+begin_src lisp
 (defun bouncer-process-approvals ()
   "Scans for APPROVED flight plans and re-injects them."
-  (let ((approved-nodes (list-objects-with-attribute :TODO "APPROVED)
+  (let ((approved-nodes (list-objects-with-attribute :TODO "APPROVED"))
         (found-any nil))
     (dolist (node approved-nodes)
       (let* ((attrs (org-object-attributes node))
@@ -102,7 +102,7 @@ The *Bouncer Skill* is the physical security layer of OpenCortex. It enforces op
             (when action
               (setf (getf action :approved) t)
               (inject-stimulus action)
-              (setf (getf (org-object-attributes node) :TODO) "DONE
+              (setf (getf (org-object-attributes node) :TODO) "DONE")
               (setq found-any t))))))
     found-any))
 #+end_src
@@ -115,9 +115,9 @@ The *Bouncer Skill* is the physical security layer of OpenCortex. It enforces op
     (harness-log "BOUNCER: Creating flight plan node '~a'..." id)
     (list :type :REQUEST :target :emacs
           :payload (list :action :insert-node :id id
-                        :attributes (list :TITLE "Flight Plan: High-Risk Action"
-                                         :TODO "PLAN" :TAGS '("FLIGHT_PLAN
-                                         :ACTION (format nil "~s" blocked-action))))))
+:attributes (list :TITLE "Flight Plan: High-Risk Action"
+                                          :TODO "PLAN" :TAGS '("FLIGHT_PLAN")
+                                          :ACTION (format nil "~s" blocked-action))))))
 #+end_src
 
 ** Gate Logic (bouncer-deterministic-gate)

skills/org-skill-config-manager.org

@@ -4,7 +4,7 @@
 #+PROPERTY: header-args:lisp :tangle org-skill-config-manager.lisp
 
 * Overview
-The *Config Manager* skill provides the OpenCortex Agent with the capability to manage its own environment variables and provider configurations.
+The *Config Manager* skill provides the OpenCortex Agent with the capability to manage its own environment variables and provider configurations. It includes an interactive setup wizard for LLM providers, gateways, and system settings.
 
 * Implementation
 
@@ -13,7 +13,7 @@ The *Config Manager* skill provides the OpenCortex Agent with the capability to
 (in-package :opencortex)
 #+end_src
 
-** Configuration Logic
+** Configuration Paths
 #+begin_src lisp
 (defun get-oc-config-dir ()
   "Returns the absolute path to the opencortex config directory."
@@ -22,19 +22,267 @@ The *Config Manager* skill provides the OpenCortex Agent with the capability to
         (uiop:ensure-directory-pathname xdg)
         (uiop:ensure-directory-pathname (merge-pathnames ".config/opencortex/" (user-homedir-pathname))))))
 
-(defun save-providers ()
-  "Stubs for saving provider configuration."
-  (harness-log "CONFIG: Providers saved."))
+(defun get-config-file ()
+  "Returns the path to the .env config file."
+  (merge-pathnames ".env" (get-oc-config-dir)))
 
-(defun configure-provider (id)
-  "Stubs for configuring a provider."
-  (harness-log "CONFIG: Configured provider ~a" id))
+(defun ensure-config-dir ()
+  "Ensures the config directory exists."
+  (let ((dir (get-oc-config-dir)))
+    (unless (uiop:directory-exists-p dir)
+      (uiop:ensure-directory-pathname dir))
+    dir))
+#+end_src
 
+** Config File Operations
+#+begin_src lisp
+(defun read-config-file ()
+  "Reads the .env config file and returns an alist of KEY=VALUE pairs."
+  (let ((config-file (get-config-file)))
+    (when (uiop:file-exists-p config-file)
+      (let ((lines (uiop:read-file-lines config-file))
+            (result nil))
+        (dolist (line lines)
+          (when (and line (> (length line) 0)
+                     (not (uiop:string-prefix-p "#" line)))
+            (let ((eq-pos (position #\= line)))
+              (when eq-pos
+                (let ((key (string-trim " " (subseq line 0 eq-pos)))
+                      (value (string-trim " " (subseq line (1+ eq-pos)))))
+                  (push (cons key value) result))))))
+        (nreverse result)))))
+
+(defun write-config-file (config-alist)
+  "Writes the config alist to the .env file."
+  (ensure-config-dir)
+  (let ((config-file (get-config-file)))
+    (with-open-file (stream config-file :direction :output :if-exists :supersede :if-does-not-exist :create)
+      (format stream "# OpenCortex Configuration~%")
+      (format stream "# Generated by opencortex setup~%~%")
+      (dolist (pair config-alist)
+        (format stream "~a=~a~%" (car pair) (cdr pair))))))
+
+(defun get-config-value (key)
+  "Gets a config value by key."
+  (let ((config (read-config-file)))
+    (cdr (assoc key config :test #'string=))))
+
+(defun set-config-value (key value)
+  "Sets a config value and saves to file."
+  (let ((config (read-config-file))
+        (pair (cons key value)))
+    (let ((existing (assoc key config :test #'string=)))
+      (if existing
+          (setf (cdr existing) value)
+          (push pair config)))
+      (write-config-file config))))
+#+end_src
+
+** Input Utilities
+#+begin_src lisp
+(defun prompt (prompt-text)
+  "Simple prompt that returns user input as a string."
+  (format t "~a" prompt-text)
+  (finish-output)
+  (read-line))
+
+(defun prompt-yes-no (prompt-text)
+  "Prompts yes/no question. Returns T for yes, nil for no."
+  (let ((response (prompt (format nil "~a [Y/n]: " prompt-text))))
+    (or (string= response "")
+        (string-equal response "Y")
+        (string-equal response "y")
+        (string-equal response "yes"))))
+
+(defun prompt-choice (prompt-text options)
+  "Prompts user to choose from a list of options. Returns the chosen option or nil."
+  (format t "~a~%" prompt-text)
+  (let ((i 1))
+    (dolist (opt options)
+      (format t "  ~a) ~a~%" i opt)
+      (incf i)))
+  (let ((response (prompt "Choice")))
+    (let ((num (ignore-errors (parse-integer response))))
+      (when (and num (<= 1 num) (>= (length options) num))
+        (nth (1- num) options)))))
+#+end_src
+
+** LLM Provider Setup
+#+begin_src lisp
+(defvar *available-providers*
+  '(("OpenAI" . "OPENAI_API_KEY")
+    ("Anthropic" . "ANTHROPIC_API_KEY")
+    ("OpenRouter" . "OPENROUTER_API_KEY")
+    ("Groq" . "GROQ_API_KEY")
+    ("Gemini" . "GEMINI_API_KEY")
+    ("Ollama (local)" . "OLLAMA_URL")))
+
+(defun setup-llm-providers ()
+  "Interactive wizard for configuring LLM providers."
+  (format t "~%~%")
+  (format t "==================================================~%")
+  (format t " LLM Provider Configuration~%")
+  (format t "==================================================~%~%")
+  
+  (let ((current-providers (loop for (name . key) in *available-providers*
+                                when (get-config-value key)
+                                collect name)))
+    (when current-providers
+      (format t "Current providers: ~{~a~^, ~}~%~%" current-providers))
+    
+    (format t "Available providers:~%")
+    (dolist (p *available-providers*)
+      (format t "  - ~a~%" (car p)))
+    (format t "~%")
+    
+    (when (prompt-yes-no "Configure a new provider?")
+      (let ((chosen (prompt-choice "Select provider:" (mapcar #'car *available-providers*))))
+        (when chosen
+          (let ((env-key (cdr (assoc chosen *available-providers* :test #'string= :key #'car))))
+            (if (string= chosen "Ollama (local)")
+                (progn
+                  (format t "Enter Ollama URL (e.g., http://localhost:11434): ")
+                  (let ((url (read-line)))
+                    (set-config-value env-key url)
+                    (format t "✓ Ollama configured at ~a~%" url))))
+                (progn
+                  (format t "Enter API key for ~a: " chosen)
+                  (let ((key (read-line)))
+                    (set-config-value env-key key)
+                    (format t "✓ ~a API key saved~%" chosen)))))))))))
+  
+  (format t "~%"))
+
+(defun setup-add-provider ()
+  "Entry point for adding a single provider (called from CLI)."
+  (setup-llm-providers))
+#+end_src
+
+** Gateway Setup
+#+begin_src lisp
+(defun setup-gateways ()
+  "Interactive wizard for configuring external gateways."
+  (format t "~%~%")
+  (format t "==================================================~%")
+  (format t " Gateway Configuration~%")
+  (format t "==================================================~%~%")
+  
+  (format t "Available gateways:~%")
+  (format t "  - Slack (https://api.slack.com/)~%")
+  (format t "  - Discord (https://discord.com/developers/)~%")
+  (format t "~%")
+  
+  (when (prompt-yes-no "Configure a gateway?")
+    (let ((chosen (prompt-choice "Select platform:" '("Slack" "Discord"))))
+      (when chosen
+        (let ((token (prompt (format nil "Enter ~a bot token: " chosen))))
+          (if (string= chosen "Slack")
+              (set-config-value "SLACK_TOKEN" token)
+              (set-config-value "DISCORD_TOKEN" token))
+          (format t "✓ ~a gateway configured~%" chosen))))))
+  
+  (format t "~%"))
+#+end_src
+
+** Skill Management
+#+begin_src lisp
+(defun setup-skills ()
+  "Interactive wizard for enabling/disabling skills."
+  (format t "~%~%")
+  (format t "==================================================~%")
+  (format t " Skill Management~%")
+  (format t "==================================================~%~%")
+  
+  (format t "Note: Skill management is not yet implemented.~%")
+  (format t "Skills are automatically loaded from ~a~%" (or (uiop:getenv "SKILLS_DIR") "default location"))
+  (format t "~%"))
+#+end_src
+
+** Memory Settings
+#+begin_src lisp
+(defun setup-memory ()
+  "Interactive wizard for memory settings."
+  (format t "~%~%")
+  (format t "==================================================~%")
+  (format t " Memory Settings~%")
+  (format t "==================================================~%~%")
+  
+  (let ((auto-save (prompt "Auto-save interval in seconds [300]:")))
+    (when (and auto-save (> (length auto-save) 0))
+      (set-config-value "MEMORY_AUTO_SAVE_INTERVAL" auto-save)))
+  
+  (let ((history (prompt "History retention in lines [1000]:")))
+    (when (and history (> (length history) 0))
+      (set-config-value "MEMORY_HISTORY_RETENTION" history)))
+  
+  (format t "✓ Memory settings saved~%")
+  (format t "~%"))
+#+end_src
+
+** Network Settings
+#+begin_src lisp
+(defun setup-network ()
+  "Interactive wizard for network settings."
+  (format t "~%~%")
+  (format t "==================================================~%")
+  (format t " Network Settings~%")
+  (format t "==================================================~%~%")
+  
+  (let ((timeout (prompt "Request timeout in seconds [30]:")))
+    (when (and timeout (> (length timeout) 0))
+      (set-config-value "REQUEST_TIMEOUT" timeout)))
+  
+  (let ((proxy (prompt "Proxy URL (leave empty for none) []:")))
+    (when (and proxy (> (length proxy) 0))
+      (set-config-value "HTTP_PROXY" proxy)))
+  
+  (format t "✓ Network settings saved~%")
+  (format t "~%"))
+#+end_src
+
+** Main Setup Wizard
+#+begin_src lisp
 (defun run-setup-wizard ()
-  "Interactive setup wizard for OpenCortex."
-  (format t "--- OpenCortex Setup Wizard ---~%")
-  (save-providers)
-  (doctor-main))
+  "Main entry point for the interactive setup wizard."
+  (format t "~%~%")
+  (format t "╔═══════════════════════════════════════════════════╗~%")
+  (format t "║         OpenCortex Setup Wizard                   ║~%")
+  (format t "╚═══════════════════════════════════════════════════╝~%")
+  (format t "~%")
+  (format t "This wizard will help you configure:~%")
+  (format t "  1. LLM Providers (OpenAI, Anthropic, etc.)~%")
+  (format t "  2. Gateway Links (Slack, Discord)~%")
+  (format t "  3. Memory Settings~%")
+  (format t "  4. Network Settings~%")
+  (format t "~%")
+  
+  (ensure-config-dir)
+  
+  ;; Step 1: LLM Providers
+  (when (prompt-yes-no "Configure LLM providers?")
+    (setup-llm-providers))
+  
+  ;; Step 2: Gateways
+  (when (prompt-yes-no "Configure gateways?")
+    (setup-gateways))
+  
+  ;; Step 3: Memory
+  (when (prompt-yes-no "Configure memory settings?")
+    (setup-memory))
+  
+  ;; Step 4: Network
+  (when (prompt-yes-no "Configure network settings?")
+    (setup-network))
+  
+  ;; Summary
+  (format t "==================================================~%")
+  (format t " Setup Complete!~%")
+  (format t "==================================================~%")
+  (format t "~%")
+  (format t "Configuration saved to: ~a~%" (get-config-file))
+  (format t "~%")
+  (format t "To verify your setup, run: opencortex doctor~%")
+  (format t "~%"))
 #+end_src
 
 ** Skill Registration
@@ -42,4 +290,4 @@ The *Config Manager* skill provides the OpenCortex Agent with the capability to
 (defskill :skill-config-manager
   :priority 100
   :trigger (lambda (ctx) (declare (ignore ctx)) nil))
-#+end_src
+#+end_src

skills/org-skill-credentials-vault.org

@@ -16,7 +16,7 @@ The *Credentials Vault* provides secure in-memory storage for sensitive API keys
 ** Vault Storage
 #+begin_src lisp
 (defvar *vault-memory* (make-hash-table :test 'equal)
-  "In-memory cache of sensitive credentials.
+  "In-memory cache of sensitive credentials.")
 #+end_src
 
 ** Secret Management
@@ -28,11 +28,11 @@ The *Credentials Vault* provides secure in-memory storage for sensitive API keys
     (if val
         val
         (let ((env-var (case provider
-                         (:gemini "GEMINI_API_KEY
-                         (:openai "OPENAI_API_KEY
-                         (:anthropic "ANTHROPIC_API_KEY
-                         (:openrouter "OPENROUTER_API_KEY
-                         (otherwise nil))))
+                          (:gemini "GEMINI_API_KEY")
+                          (:openai "OPENAI_API_KEY")
+                          (:anthropic "ANTHROPIC_API_KEY")
+                          (:openrouter "OPENROUTER_API_KEY")
+                          (otherwise nil))))
           (when env-var (uiop:getenv env-var))))))
 
 (defun vault-set-secret (provider secret &key (type :api-key))

skills/org-skill-diagnostics.org

@@ -4,64 +4,249 @@
 #+PROPERTY: header-args:lisp :tangle org-skill-diagnostics.lisp
 
 * Overview
-The *Diagnostics Skill* (Doctor) provides system-wide health checks and dependency verification.
+The *Diagnostics Skill* (Doctor) provides system-wide health checks and dependency verification. It validates external dependencies, XDG environment, and LLM provider connectivity.
 
-* Implementation
+* Phase A: Demand (Thinking)
+** Why a Doctor?
+The Doctor transforms opaque startup failures into actionable engineering reports. It ensures the Brain never attempts to boot in a compromised state.
+
+** Detection Invariant
+Binary detection must use shell probing (`which`) to account for varying `$PATH` inheritance between interactive and headless sessions.
+
+* Phase B: Protocol (Success Criteria)
+- Dependency check passes when all required binaries are found
+- Environment check passes when XDG directories exist and are accessible
+- LLM check passes when at least one provider is configured or Ollama is running locally
+
+* Phase C: Implementation (Build)
 
 ** Package Context
 #+begin_src lisp
 (in-package :opencortex)
 #+end_src
 
-** Dependency Check (doctor-check-dependencies)
+** Global Configuration
+#+begin_src lisp
+(defvar *doctor-required-binaries* '("sbcl" "emacs" "git" "socat" "nc")
+  "List of external binaries required for full system operation.")
+
+(defvar *doctor-package-map*
+  '(("sbcl" . "sbcl")
+    ("emacs" . "emacs")
+    ("git" . "git")
+    ("socat" . "socat")
+    ("nc" . "netcat-openbsd")
+    ("curl" . "curl")
+    ("rlwrap" . "rlwrap"))
+  "Map binary names to apt package names.")
+
+(defvar *doctor-missing-deps* nil
+  "List of missing dependencies populated by doctor-check-dependencies.")
+
+(defvar *doctor-auto-install* t
+  "When T, doctor will attempt to install missing dependencies automatically.")
+#+end_src
+
+** Dependency Verification
 #+begin_src lisp
 (defun doctor-check-dependencies ()
-  "Verifies that all required external binaries are available."
-  (let ((deps '("sbcl" "emacs" "git" "curl" "nc"))
-        (all-ok t))
-    (format t "DOCTOR: Checking System Dependencies...~%")
-    (dolist (dep deps)
-      (if (uiop:run-program (list "which" dep) :ignore-error-status t)
-          (format t "  [OK] Found ~a~%" dep)
-          (progn
-            (format t "  [FAIL] Missing ~a~%" dep)
-            (setf all-ok nil))))
+  "Verifies that required external binaries are available in the PATH via shell probe."
+  (setf *doctor-missing-deps* nil)
+  (let ((all-ok t))
+    (format t "DOCTOR: Checking system dependencies...~%")
+    (dolist (dep *doctor-required-binaries*)
+      (let ((path (ignore-errors
+                    (uiop:run-program (list "which" dep)
+                                      :output :string :ignore-error-status t))))
+        (if (and path (> (length path) 0))
+            (format t "  [OK] Found ~a~%" dep)
+            (progn
+              (format t "  [FAIL] Missing binary: ~a~%" dep)
+              (push dep *doctor-missing-deps*)
+              (setf all-ok nil)))))
+    (when (and all-ok (null *doctor-missing-deps*))
+      (format t "DOCTOR: All dependencies satisfied.~%"))
     all-ok))
 #+end_src
 
-** XDG Check (doctor-check-xdg)
+** Auto-Install Dependencies
 #+begin_src lisp
-(defun doctor-check-xdg ()
-  "Verifies XDG environment variables and directory structure."
-  (format t "DOCTOR: Checking XDG environment...~%")
-  (let ((vars '("OC_CONFIG_DIR" "OC_DATA_DIR" "OC_STATE_DIR" "MEMEX_DIR")))
-    (dolist (var vars)
-      (let ((val (uiop:getenv var)))
-        (if val
-            (format t "  [OK] ~a: ~a~%" var val)
-            (format t "  [WARN] ~a is not set.~%" var)))))
-  t)
+(defun doctor-install-dependencies ()
+  "Attempts to install missing system dependencies via apt."
+  (when (null *doctor-missing-deps*)
+    (format t "DOCTOR: No missing dependencies to install.~%")
+    (return-from doctor-install-dependencies t))
+
+  (format t "DOCTOR: Attempting to install ~a missing dependencies...~%" (length *doctor-missing-deps*))
+
+  (let ((packages (remove-duplicates
+                   (mapcar (lambda (dep)
+                             (or (cdr (assoc dep *doctor-package-map* :test #'string=))
+                                 dep))
+                           *doctor-missing-deps*)
+                   :test #'string=)))
+    (format t "DOCTOR: Packages to install: ~a~%" packages)
+
+    (let ((cmd (format nil "apt-get install -y ~{~a~^ ~}" packages)))
+      (format t "DOCTOR: Running: ~a~%" cmd)
+      (handler-case
+          (let ((output (uiop:run-program cmd
+                                           :output :string
+                                           :error-output :string
+                                           :external-format :utf-8)))
+            (if (zerop (uiop:run-program (format nil "which ~a" (car *doctor-missing-deps*))
+                                          :ignore-error-status t))
+                (progn
+                  (format t "DOCTOR: Dependencies installed successfully.~%")
+                  (setf *doctor-missing-deps* nil)
+                  t)
+                (progn
+                  (format t "DOCTOR: Installation failed. Output: ~a~%" output)
+                  nil)))
+        (error (c)
+          (format t "DOCTOR: Installation error: ~a~%" c)
+          nil)))))
 #+end_src
 
-** Main Diagnostic (doctor-main)
+** XDG Environment Validation
+#+begin_src lisp
+(defun doctor-check-env ()
+  "Validates XDG directories and environment configuration."
+  (format t "DOCTOR: Checking XDG environment...~%")
+  (let ((all-ok t)
+        (config-dir (uiop:getenv "OC_CONFIG_DIR"))
+        (data-dir (uiop:getenv "OC_DATA_DIR"))
+        (state-dir (uiop:getenv "OC_STATE_DIR"))
+        (memex-dir (uiop:getenv "MEMEX_DIR")))
+
+    (flet ((check-dir (name path critical)
+             (if (and path (> (length path) 0))
+                 (if (uiop:directory-exists-p path)
+                     (format t "  [OK] ~a: ~a~%" name path)
+                     (progn
+                       (format t "  [FAIL] ~a directory missing: ~a~%" name path)
+                       (when critical (setf all-ok nil))))
+                 (progn
+                   (format t "  [FAIL] ~a variable not set.~%" name)
+                   (when critical (setf all-ok nil))))))
+
+      (check-dir "Config (OC_CONFIG_DIR)" config-dir t)
+      (check-dir "Data (OC_DATA_DIR)" data-dir t)
+      (check-dir "State (OC_STATE_DIR)" state-dir t)
+      (check-dir "Memex (MEMEX_DIR)" memex-dir t))
+    all-ok))
+#+end_src
+
+** LLM Connectivity
+The doctor checks all supported LLM providers and detects local Ollama instances.
+
+#+begin_src lisp
+(defun doctor-check-llm ()
+  "Tests connectivity to LLM providers. Returns T if at least one provider is configured."
+  (format t "DOCTOR: Checking LLM connectivity...~%")
+  (let ((providers '((:openrouter . "OPENROUTER_API_KEY")
+                    (:anthropic . "ANTHROPIC_API_KEY")
+                    (:openai . "OPENAI_API_KEY")
+                    (:groq . "GROQ_API_KEY")
+                    (:gemini . "GEMINI_API_KEY")
+                    (:ollama . "OLLAMA_URL")))
+        (configured nil))
+    (dolist (p providers)
+      (let ((env-val (uiop:getenv (cdr p))))
+        (cond
+          ((and env-val (> (length env-val) 0))
+           (format t "  [OK] ~a configured~%" (car p))
+           (setf configured t))
+          ((eq (car p) :ollama)
+           (let ((ollama-check (ignore-errors
+                                 (uiop:run-program '("curl" "-s" "http://localhost:11434/api/tags")
+                                                    :output :string :ignore-error-status t))))
+             (when (and ollama-check (search "\"models\"" ollama-check))
+               (format t "  [OK] Ollama local model server detected~%")
+               (setf configured t)))))))
+    (if configured
+        (progn
+          (format t "  [OK] LLM provider(s) available~%")
+          t)
+        (progn
+          (format t "  [WARN] No LLM provider configured.~%")
+          (format t "  Run 'opencortex setup' to configure a provider.~%")
+          t))))
+#+end_src
+
+** Orchestration
+#+begin_src lisp
+(defun doctor-run-all (&key (auto-install t))
+  "Executes the full diagnostic suite and returns T if system is healthy."
+  (format t "==================================================~%")
+  (format t " OPENCORTEX DOCTOR: Commencing Health Check~%")
+  (format t "==================================================~%")
+  (let ((dep-ok (doctor-check-dependencies)))
+    (when (and (not dep-ok) auto-install *doctor-auto-install*)
+      (format t "DOCTOR: Attempting automatic installation...~%")
+      (setf dep-ok (doctor-install-dependencies))
+      (when dep-ok
+        (setf dep-ok (doctor-check-dependencies))))
+    (let ((env-ok (doctor-check-env))
+          (llm-ok (doctor-check-llm)))
+      (format t "==================================================~%")
+      (if (and dep-ok env-ok)
+          (progn
+            (format t " ✓ SYSTEM HEALTHY: Ready for ignition.~%")
+            t)  ;; Explicitly return T
+          (progn
+            (format t "==================================================~%")
+            (format t " ISSUES FOUND:~%")
+            (when (not dep-ok)
+              (format t "  - Missing system dependencies~%"))
+            (when (not llm-ok)
+              (format t "  - No LLM provider configured~%"))
+            (format t "~%")
+            (format t " RECOMMENDED ACTIONS:~%")
+            (format t "  1. Run 'opencortex setup' to configure everything~%")
+            (format t "  2. Or run 'opencortex doctor --fix' for auto-repair~%")
+            (format t "==================================================~%")
+            nil)))))  ;; Return nil when issues found
+#+end_src
+
+** CLI Entry Point
 #+begin_src lisp
 (defun doctor-main ()
-  "Runs all diagnostic checks."
-  (format t "==================================================~%")
-  (format t " OpenCortex System Diagnostic~%")
-  (format t "==================================================~%")
-  (let ((d-ok (doctor-check-dependencies))
-        (x-ok (doctor-check-xdg)))
-    (format t "==================================================~%")
-    (if (and d-ok x-ok)
-        (format t " ✓ SYSTEM HEALTHY: Ready for ignition.~%")
-        (format t " ✗ SYSTEM UNHEALTHY: Issues detected.~%"))))
+  "Entry point for the 'doctor' CLI command."
+  (if (doctor-run-all)
+      (uiop:quit 0)
+      (uiop:quit 1)))
 #+end_src
 
+* Phase D: Verification (Testing)
+
+** Dependency Test
+#+begin_src lisp :tangle no
+(test test-doctor-dependency-check
+  "Verify that missing binaries are correctly identified as failures."
+  (let ((opencortex::*doctor-required-binaries* '("non-existent-binary-123")))
+    (is (null (opencortex:doctor-check-dependencies)))))
+#+end_src
+
+** Environment Test
+#+begin_src lisp :tangle no
+(test test-doctor-env-check
+  "Verify that an invalid MEMEX_DIR triggers a critical failure."
+  (let ((old-m (uiop:getenv "MEMEX_DIR")))
+    (unwind-protect
+         (progn
+           (setf (uiop:getenv "MEMEX_DIR") "/non/existent/path/999")
+           (is (null (opencortex:doctor-check-env))))
+      (setf (uiop:getenv "MEMEX_DIR") (or old-m "")))))
+#+end_src
+
+* Phase E: Lifecycle
+The doctor skill should be loaded early (priority 100) to validate system health before other skills initialize.
+
 ** Skill Registration
 #+begin_src lisp
 (defskill :skill-diagnostics
   :priority 100
   :trigger (lambda (ctx) (eq (getf (getf ctx :payload) :sensor) :heartbeat))
   :deterministic (lambda (action ctx) (declare (ignore action ctx)) nil))
-#+end_src
+#+end_src