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

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