fix(queue): add --format=json and --limit flags to queue list

- kugetsu: show only parent commands, not all subcommands inline
- kugetsu <command> help: show help for specific command
- kugetsu queue: show queue subcommands (list, stats, clear, enqueue)
- kugetsu queue-daemon: show daemon subcommands (start, stop, restart, status, logs)
- kugetsu env: show env subcommands (list, get, set, rm)
- kugetsu server: show server subcommands (list, add, remove, default, get)

Closes #244

skills/kugetsu/scripts/kugetsu

@@ -17,77 +17,129 @@ usage() {
 kugetsu - OpenCode Session Manager (Issue-Driven)
 
 Usage:
-    kugetsu init [--force]                            Initialize base + pm-agent sessions (requires TTY)
-    kugetsu start <issue-ref> <message> [--debug]    Start task for issue (forks base session)
-    kugetsu continue <issue-ref> [message] [--debug] Continue existing task for issue
-    kugetsu delegate <message>                        Send message to PM agent (fire-and-forget)
-    kugetsu logs [n]                                  Show recent delegation logs (default: 10)
-    kugetsu status                                    Check kugetsu initialization status
-    kugetsu doctor [--fix]                            Diagnose and fix kugetsu issues
-    kugetsu notify [list|clear]                        Show or clear notifications
-    kugetsu list                                     List all tracked sessions
-    kugetsu prune [--force]                          Remove orphaned sessions (keeps base + pm-agent)
-    kugetsu destroy <issue-ref> [-y]                  Delete session for issue
-    kugetsu destroy --pm-agent [-y]                   Delete pm-agent session (not recommended)
-    kugetsu destroy --base [-y]                      Delete base session
-    kugetsu set-pr <issue-ref> <pr-url>            Set PR URL for session (for PR tracking)
-    kugetsu context <issue-ref>                        Show context for issue
-    kugetsu queue [list|stats|clear]                  Show queue status or statistics
-    kugetsu queue enqueue <issue-ref> <message>       Enqueue a task (normally via delegate)
-    kugetsu queue-daemon [start|stop|restart|status|logs]  Manage queue daemon
-    kugetsu env [get|set|list]                        Manage agent environment variables
-    kugetsu server [list|add|remove|default|get]     Manage git server configurations
-    kugetsu help                                     Show this help
+    kugetsu <command> [subcommand] [options]
+
+Commands:
+    init [--force]                                    Initialize base + pm-agent sessions (requires TTY)
+    start <issue-ref> <message> [--debug]            Start task for issue (forks base session)
+    continue <issue-ref> [message] [--debug]          Continue existing task for issue
+    delegate <message>                                Send message to PM agent (fire-and-forget)
+    logs [n]                                          Show recent delegation logs (default: 10)
+    status                                            Check kugetsu initialization status
+    doctor [--fix]                                    Diagnose and fix kugetsu issues
+    notify [list|clear]                               Show or clear notifications
+    list                                              List all tracked sessions
+    prune [--force]                                  Remove orphaned sessions
+    destroy <target> [-y]                             Delete session (issue, pm-agent, or base)
+    set-pr <issue-ref> <pr-url>                       Set PR URL for session
+    context <issue-ref>                               Show context for issue
+    queue [subcommand]                                Queue management
+    queue-daemon [subcommand]                         Queue daemon management
+    env [subcommand]                                  Environment variable management
+    server [subcommand]                                Git server configuration
+    help [command]                                   Show help for a command
+
+Use 'kugetsu <command> help' for subcommand help.
+Example: kugetsu queue help, kugetsu queue-daemon help
 
 Issue Ref Format:
     instance/user/repo#number
     Example: github.com/shoko/kugetsu#14
+EOF
+}
 
-Commands:
-    init        Create base + pm-agent sessions via TUI. Requires terminal access.
-                Use --force to reinitialize if sessions exist.
-    start       Fork new session from base for specific issue.
-                Requires pm-agent to be running (created by init).
-    continue    Continue work on existing issue session.
-    delegate    Send message to PM agent for task coordination.
-                Fire-and-forget: returns immediately, runs in background.
-                Use 'kugetsu logs' to check output.
-    logs        Show recent delegation logs.
-                Default: 10 most recent. Use 'kugetsu logs 20' for more.
-    status      Check if kugetsu is initialized and PM agent is active.
-    doctor      Diagnose kugetsu issues. Use --fix to attempt repairs.
-    notify      Show or clear notifications from PM agent.
-                Use 'kugetsu notify list' to see unread notifications.
-    list        Show all sessions (base + pm-agent + forked issues).
-    prune       Remove sessions not in index (orphaned from opencode).
-                Use --force to skip confirmation.
-    destroy     Delete specific issue, pm-agent, or base session.
+usage_queue() {
+    cat << 'EOF'
+kugetsu queue - Queue management
 
-Options:
-    --debug   Show real-time debug output and capture to debug.log
+Usage:
+    kugetsu queue [subcommand]
 
-PM Context:
-    kugetsu reads ~/.kugetsu/pm-agent.md (if exists) and injects it
-    into the PM agent session at init time. This allows customizing PM
-    behavior without recreating the session.
+Subcommands:
+    list [--limit=N] [--format=json]                 Show pending tasks (default: 10 items, text format)
+    stats                                              Show queue statistics
+    clear                                              Clear all queue items
+    enqueue <issue-ref> <message>                      Enqueue a task
+    help                                               Show this help
 
-Notifications:
-    PM Agent writes task completion notifications to ~/.kugetsu/notifications.json
-    Use 'kugetsu notify list' to see unread notifications.
+Options for list:
+    --limit=N         Number of items to return (default: 10)
+    --format=json     Output in JSON format with stats
 
 Examples:
-    kugetsu init
-    kugetsu status
-    kugetsu delegate "work on issue #5"
-    kugetsu logs
-    kugetsu logs 20
-    kugetsu doctor
-    kugetsu doctor --fix
-    kugetsu notify list
-    kugetsu notify clear
-    kugetsu start github.com/shoko/kugetsu#14 "fix bug"
-    kugetsu continue github.com/shoko/kugetsu#14 "add tests"
-    kugetsu list
+    kugetsu queue list
+    kugetsu queue list --limit=50
+    kugetsu queue list --format=json
+    kugetsu queue list --limit=20 --format=json
+    kugetsu queue stats
+    kugetsu queue clear
+    kugetsu queue enqueue github.com/shoko/kugetsu#14 "fix bug"
+EOF
+}
+
+usage_queue_daemon() {
+    cat << 'EOF'
+kugetsu queue-daemon - Queue daemon management
+
+Usage:
+    kugetsu queue-daemon [subcommand]
+
+Subcommands:
+    start                                              Start the queue daemon
+    stop                                               Stop the queue daemon
+    restart                                            Restart the queue daemon
+    status                                             Check daemon status
+    logs                                               Show recent daemon logs
+    help                                               Show this help
+
+Examples:
+    kugetsu queue-daemon start
+    kugetsu queue-daemon status
+    kugetsu queue-daemon logs
+EOF
+}
+
+usage_env() {
+    cat << 'EOF'
+kugetsu env - Environment variable management
+
+Usage:
+    kugetsu env [subcommand]
+
+Subcommands:
+    list                                               List all environment variables
+    get <key>                                          Get a specific variable
+    set <key> <value>                                  Set a variable
+    rm <key>                                           Remove a variable
+    help                                               Show this help
+
+Examples:
+    kugetsu env list
+    kugetsu env get GITEA_TOKEN
+    kugetsu env set CUSTOM_VAR "value"
+    kugetsu env rm CUSTOM_VAR
+EOF
+}
+
+usage_server() {
+    cat << 'EOF'
+kugetsu server - Git server configuration
+
+Usage:
+    kugetsu server [subcommand]
+
+Subcommands:
+    list                                               List all configured servers (default)
+    add <name> <url>                                   Add a new server
+    remove <name>                                      Remove a server
+    default [<name>]                                   Get or set default server
+    get [<name>]                                       Get server URL
+    help                                               Show this help
+
+Examples:
+    kugetsu server list
+    kugetsu server add github.com https://github.com
+    kugetsu server default github.com
 EOF
 }
 
@@ -310,19 +362,25 @@ PYEOF
 
 get_pending_tasks() {
     local limit="${1:-10}"
+    local format="${2:-text}"
     
     if [ ! -d "$QUEUE_ITEMS_DIR" ]; then
-        echo "[]"
+        if [ "$format" = "json" ]; then
+            echo '{"items": [], "total": 0, "pending": 0}'
+        else
+            echo "No pending tasks in queue."
+        fi
         return
     fi
     
-    python3 -c "
+    python3 << PYEOF
 import json
 import os
 import sys
 
 queue_dir = os.environ.get('QUEUE_ITEMS_DIR', '')
 limit = int(sys.argv[1]) if len(sys.argv) > 1 else 10
+format_type = sys.argv[2] if len(sys.argv) > 2 else 'text'
 
 items = []
 if os.path.isdir(queue_dir):
@@ -334,13 +392,27 @@ if os.path.isdir(queue_dir):
                     data = json.load(f)
                     if data.get('state') == 'pending':
                         items.append(data)
-                        if len(items) >= limit:
-                            break
             except:
                 pass
 
-print(json.dumps(items))
-" "$limit"
+items.sort(key=lambda x: x.get('pending_since', ''))
+
+if format_type == 'json':
+    output = {
+        "items": items[:limit],
+        "total": len(items),
+        "pending": len(items)
+    }
+    print(json.dumps(output))
+else:
+    if not items:
+        print("No pending tasks in queue.")
+    else:
+        print("Pending tasks:")
+        for t in items[:limit]:
+            msg = t.get('message', '')[:50]
+            print(f"  {t.get('id')}: {t.get('issue_ref')} - {msg}...")
+PYEOF
 }
 
 get_queue_stats() {
@@ -865,18 +937,34 @@ find_sessions_by_issue_number() {
 }
 
 cmd_queue() {
-    local action="${1:-list}"
-    shift
+    local action="${1:-}"
     
     case "$action" in
+        ""|help|--help|-h)
+            usage_queue
+            ;;
+        help|--help|-h)
+            usage_queue
+            ;;
         list)
-            local pending_tasks=$(get_pending_tasks 10)
-            if [ "$pending_tasks" = "[]" ]; then
-                echo "No pending tasks in queue."
-            else
-                echo "Pending tasks:"
-                echo "$pending_tasks" | python3 -c "import sys, json; [print(f\"  {t.get('id')}: {t.get('issue_ref')} - {t.get('message', '')[:50]}...\") for t in json.load(sys.stdin)]"
-            fi
+            local limit="10"
+            local format="text"
+            
+            while [ $# -gt 0 ]; do
+                case "$1" in
+                    --limit=*)
+                        limit="${1#*=}"
+                        ;;
+                    --format=json)
+                        format="json"
+                        ;;
+                    *)
+                        ;;
+                esac
+                shift
+            done
+            
+            get_pending_tasks "$limit" "$format"
             ;;
         stats)
             local stats=$(get_queue_stats)
@@ -898,8 +986,8 @@ cmd_queue() {
             echo "Queue cleared."
             ;;
         enqueue)
-            local issue_ref="${1:-}"
-            local message="${2:-}"
+            local issue_ref="${2:-}"
+            local message="${3:-}"
             if [ -z "$issue_ref" ] || [ -z "$message" ]; then
                 echo "Usage: kugetsu queue enqueue <issue-ref> <message>" >&2
                 exit 1
@@ -910,16 +998,20 @@ cmd_queue() {
             check_task_timeouts
             ;;
         *)
-            echo "Usage: kugetsu queue [list|stats|clear|enqueue]" >&2
+            echo "Unknown queue subcommand: $action" >&2
+            usage_queue
             exit 1
             ;;
     esac
 }
 
 cmd_queue_daemon() {
-    local action="${1:-status}"
+    local action="${1:-}"
     
     case "$action" in
+        ""|help|--help|-h)
+            usage_queue_daemon
+            ;;
         start)
             if [ -f "$QUEUE_DAEMON_PID_FILE" ]; then
                 local old_pid=$(cat "$QUEUE_DAEMON_PID_FILE")
@@ -978,7 +1070,8 @@ cmd_queue_daemon() {
             fi
             ;;
         *)
-            echo "Usage: kugetsu queue-daemon [start|stop|restart|status|logs]" >&2
+            echo "Unknown queue-daemon subcommand: $action" >&2
+            usage_queue_daemon
             exit 1
             ;;
     esac
@@ -1059,10 +1152,12 @@ set_debug_mode() {
 }
 
 cmd_env() {
-    local action="${1:-list}"
-    shift
+    local action="${1:-}"
     
     case "$action" in
+        ""|help|--help|-h)
+            usage_env
+            ;;
         list)
             echo "Agent environment variables:"
             if [ -d "$ENV_DIR" ]; then
@@ -1080,7 +1175,7 @@ cmd_env() {
             fi
             ;;
         get)
-            local key="${1:-}"
+            local key="${2:-}"
             if [ -z "$key" ]; then
                 echo "Usage: kugetsu env get <key>" >&2
                 exit 1
@@ -1095,8 +1190,8 @@ cmd_env() {
             fi
             ;;
         set)
-            local key="${1:-}"
-            local value="${2:-}"
+            local key="${2:-}"
+            local value="${3:-}"
             if [ -z "$key" ] || [ -z "$value" ]; then
                 echo "Usage: kugetsu env set <key> <value>" >&2
                 exit 1
@@ -1105,8 +1200,8 @@ cmd_env() {
             echo "${key}=${value}" >> "$ENV_DIR/default.env"
             echo "Set $key in $ENV_DIR/default.env"
             ;;
-        rm)
-            local key="${1:-}"
+        rm|remove)
+            local key="${2:-}"
             if [ -z "$key" ]; then
                 echo "Usage: kugetsu env rm <key>" >&2
                 exit 1
@@ -1117,7 +1212,8 @@ cmd_env() {
             fi
             ;;
         *)
-            echo "Usage: kugetsu env [list|get|set|rm]" >&2
+            echo "Unknown env subcommand: $action" >&2
+            usage_env
             exit 1
             ;;
     esac
@@ -1127,7 +1223,10 @@ cmd_server() {
     local action="${1:-}"
     
     case "$action" in
-        ""|"list")
+        ""|help|--help|-h)
+            usage_server
+            ;;
+        "list")
             if [ -z "${GIT_SERVERS+x}" ]; then
                 echo "No git servers configured"
                 return
@@ -1204,14 +1303,8 @@ cmd_server() {
             fi
             ;;
         *)
-            echo "Usage: kugetsu server <list|add|remove|default|get>" >&2
-            echo "" >&2
-            echo "Commands:" >&2
-            echo "  list              List all configured git servers" >&2
-            echo "  add <name> <url>  Add a new git server" >&2
-            echo "  remove <name>     Remove a git server" >&2
-            echo "  default [<name>]  Get or set default server" >&2
-            echo "  get [<name>]      Get URL for a server (default: current default)" >&2
+            echo "Unknown server subcommand: $action" >&2
+            usage_server
             exit 1
             ;;
     esac
@@ -1321,8 +1414,30 @@ main() {
     
     case "$command" in
         help|--help|-h)
+            local subcommand="${1:-}"
+            case "$subcommand" in
+                queue|"")
+                    usage_queue
+                    ;;
+                queue-daemon)
+                    usage_queue_daemon
+                    ;;
+                env)
+                    usage_env
+                    ;;
+                server)
+                    usage_server
+                    ;;
+                "")
                     usage
                     ;;
+                *)
+                    echo "Help not available for '$subcommand'" >&2
+                    usage
+                    exit 1
+                    ;;
+            esac
+            ;;
         init)
             cmd_init "$@"
             ;;

skills/kugetsu/scripts/kugetsu-config.sh

@@ -26,6 +26,9 @@ QUEUE_DAEMON_INTERVAL_MINUTES="${QUEUE_DAEMON_INTERVAL_MINUTES:-5}"
 QUEUE_CLEANUP_AGE_DAYS="${QUEUE_CLEANUP_AGE_DAYS:-7}"
 TASK_TIMEOUT_HOURS="${TASK_TIMEOUT_HOURS:-1}"
 
+NETWORK_RETRY_ATTEMPTS="${NETWORK_RETRY_ATTEMPTS:-3}"
+NETWORK_RETRY_DELAY_SECONDS="${NETWORK_RETRY_DELAY_SECONDS:-5}"
+
 # Load user config overrides (~/.kugetsu/config)
 if [ -f "$KUGETSU_DIR/config" ]; then
     source "$KUGETSU_DIR/config"
@@ -87,3 +90,24 @@ set_debug_mode() {
     
     echo "${filtered_args[@]}"
 }
+
+retry_with_backoff() {
+    local max_attempts="${1:-$NETWORK_RETRY_ATTEMPTS}"
+    local delay_seconds="${2:-$NETWORK_RETRY_DELAY_SECONDS}"
+    local command="$3"
+    local remaining_attempts=$max_attempts
+    
+    while [ $remaining_attempts -gt 0 ]; do
+        if eval "$command"; then
+            return 0
+        fi
+        remaining_attempts=$((remaining_attempts - 1))
+        if [ $remaining_attempts -gt 0 ]; then
+            log "warn" "retry_with_backoff" "Command failed, $remaining_attempts retries remaining. Waiting ${delay_seconds}s..."
+            sleep "$delay_seconds"
+            delay_seconds=$((delay_seconds * 2))
+        fi
+    done
+    log "error" "retry_with_backoff" "Command failed after $max_attempts attempts"
+    return 1
+}

skills/kugetsu/scripts/kugetsu-index.sh

@@ -139,6 +139,77 @@ validate_issue_ref() {
     fi
 }
 
+read_json_file() {
+    local file_path="$1"
+    if [ -f "$file_path" ]; then
+        cat "$file_path"
+    else
+        echo "{}"
+    fi
+}
+
+write_json_file() {
+    local file_path="$1"
+    local json_content="$2"
+    local temp_file="$file_path.tmp.$$"
+    
+    printf '%s' "$json_content" > "$temp_file"
+    
+    if ! python3 -c "import json; json.load(open('$temp_file'))" 2>/dev/null; then
+        echo "Error: write_json_file would create malformed JSON: $file_path" >&2
+        rm -f "$temp_file"
+        return 1
+    fi
+    
+    mv "$temp_file" "$file_path"
+}
+
+get_json_value() {
+    local file_path="$1"
+    local key="$2"
+    local default="${3:-}"
+    
+    if [ ! -f "$file_path" ]; then
+        echo "$default"
+        return
+    fi
+    
+    python3 -c "import json; print(json.load(open('$file_path')).get('$key', '$default'))" 2>/dev/null || echo "$default"
+}
+
+set_json_value() {
+    local file_path="$1"
+    local key="$2"
+    local value="$3"
+    
+    if [ ! -f "$file_path" ]; then
+        printf '{"%s": "%s"}\n' "$key" "$value" > "$file_path"
+        return
+    fi
+    
+    python3 << PYEOF
+import json
+import sys
+
+file_path = "$file_path"
+key = "$key"
+value = "$value"
+
+try:
+    with open(file_path, 'r') as f:
+        data = json.load(f)
+except:
+    data = {}
+
+data[key] = value
+
+with open(file_path, 'w') as f:
+    json.dump(data, f, indent=2)
+
+print(f"Set $key = $value in $file_path")
+PYEOF
+}
+
 update_session_pr_url() {
     local issue_ref="$1"
     local pr_url="$2"

skills/kugetsu/scripts/kugetsu-queue-daemon.sh

@@ -34,6 +34,8 @@ release_lock() {
 check_task_completion() {
     local item="$1"
     local queue_id=$(basename "$item" .json)
+    
+    local item_data=$(read_json_file "$item")
     local state=$(python3 -c "import json; print(json.load(open('$item')).get('state', ''))" 2>/dev/null)
 
     [ "$state" = "notified" ] || return 0
@@ -41,6 +43,31 @@ check_task_completion() {
     local session_id=$(python3 -c "import json; print(json.load(open('$item')).get('opencode_session_id', ''))" 2>/dev/null)
     local issue_ref=$(python3 -c "import json; print(json.load(open('$item')).get('issue_ref', ''))" 2>/dev/null)
     local pid=$(python3 -c "import json; print(json.load(open('$item')).get('pid', ''))" 2>/dev/null)
+    local notified_at=$(python3 -c "import json; print(json.load(open('$item')).get('notified_at', ''))" 2>/dev/null)
+
+    local timed_out=false
+    if [ -n "$notified_at" ]; then
+        local notified_epoch=$(date -d "$notified_at" +%s 2>/dev/null || echo "0")
+        local now_epoch=$(date +%s)
+        local hours_elapsed=$(( (now_epoch - notified_epoch) / 3600 ))
+        if [ "$hours_elapsed" -ge "${TASK_TIMEOUT_HOURS:-1}" ]; then
+            timed_out=true
+            log_warn "queue-daemon" "Task $queue_id ($issue_ref) timed out after ${hours_elapsed}h"
+        fi
+    fi
+
+    if [ "$timed_out" = true ]; then
+        if [ -n "$pid" ] && [ "$pid" != "None" ]; then
+            kill "$pid" 2>/dev/null || true
+        fi
+        if [ -n "$session_id" ]; then
+            opencode session stop "$session_id" 2>/dev/null || true
+        fi
+        update_queue_item_state "$queue_id" "error"
+        log_error "queue-daemon" "Task $queue_id ($issue_ref) marked error — timeout after ${hours_elapsed}h"
+        release_lock "$issue_ref"
+        return
+    fi
 
     if [ -n "$pid" ] && [ "$pid" != "None" ]; then
         if ! kill -0 "$pid" 2>/dev/null; then

skills/kugetsu/scripts/kugetsu-session.sh

@@ -13,7 +13,8 @@ count_active_dev_sessions() {
     if [ -d "$SESSIONS_DIR" ]; then
         for session_file in "$SESSIONS_DIR"/*.json; do
             if [ -f "$session_file" ]; then
-                local filename=$(basename "$session_file")
+                local filename
+                filename=$(basename "$session_file")
                 if [ "$filename" != "base.json" ] && [ "$filename" != "pm-agent.json" ]; then
                     count=$((count + 1))
                 fi
@@ -239,23 +240,55 @@ create_session() {
         return 1
     fi
     
-    local before_json=$(opencode session list --format=json 2>/dev/null)
-    local before_set=$(echo "$before_json" | python3 -c "import sys,json; sessions=json.load(sys.stdin); print('|'.join(s['id'] for s in sessions))" 2>/dev/null || echo "|")
+    local before_file
+    before_file="$KUGETSU_DIR/sessions/before$$.json"
+    local after_file
+    after_file="$KUGETSU_DIR/sessions/after$$.json"
     
-    opencode run --fork --session "$base_session" "new session" >/dev/null 2>&1
+    opencode session list --format=json > "$before_file" 2>/dev/null || printf '{}' > "$before_file"
+    
+    local fork_success=false
+    local attempt=0
+    local max_attempts="${NETWORK_RETRY_ATTEMPTS:-3}"
+    
+    while [ $attempt -lt $max_attempts ] && [ "$fork_success" = false ]; do
+        attempt=$((attempt + 1))
+        if opencode run --fork --session "$base_session" "new session" >/dev/null 2>&1; then
+            fork_success=true
+        elif [ $attempt -lt $max_attempts ]; then
+            log "warn" "create_session" "Fork attempt $attempt failed, retrying..."
+            sleep "$((attempt * 2))"
+        fi
+    done
+    
+    if [ "$fork_success" = false ]; then
+        log "error" "create_session" "Failed to fork session after $max_attempts attempts"
+        rm -f "$before_file" "$after_file"
+        return 1
+    fi
     
     sleep 1
     
-    local after_json=$(opencode session list --format=json 2>/dev/null)
-    local after_sessions=$(echo "$after_json" | python3 -c "import sys,json; sessions=json.load(sys.stdin); [print(s['id']) for s in sessions]" 2>/dev/null || true)
+    opencode session list --format=json > "$after_file" 2>/dev/null || printf '{}' > "$after_file"
     
-    local new_session_id=""
-    while IFS= read -r sess; do
-        if [[ -n "$sess" ]] && [[ ! "$before_set" =~ \|${sess}\| ]]; then
-            new_session_id="$sess"
+    local new_session_id
+    new_session_id=$(python3 << PYEOF
+import json
+
+with open("$before_file", 'r') as f:
+    before = json.load(f)
+with open("$after_file", 'r') as f:
+    after = json.load(f)
+
+before_ids = set(s['id'] for s in before)
+for s in after:
+    if s['id'] not in before_ids:
+        print(s['id'])
         break
-        fi
-    done <<< "$after_sessions"
+PYEOF
+)
+    
+    rm -f "$before_file" "$after_file"
     
     echo "$new_session_id"
 }
@@ -270,50 +303,37 @@ build_dev_agent_message() {
     local number=$(echo "$issue_ref" | grep -oE '#[0-9]+$' | tr -d '#')
     local worktree_path=$(issue_ref_to_worktree_path "$issue_ref")
     
+    local conflict_check=""
+    local review_notes=""
+    local delegator_header=""
+    local delegator_footer=""
     if [ -n "$user_message" ]; then
-        cat <<EOF
-You are assigned to work on $issue_ref.
+        conflict_check="   - CRITICAL: Check if PR has merge conflicts before asking for review:
+     - Use: curl -s \"https://$instance/api/v1/repos/$owner/$repo/pulls/$number\" -H \"Authorization: Bearer \$GITEA_TOKEN\"
+     - If \"mergeable\": false, there ARE conflicts - you MUST resolve them FIRST
+     - To resolve: cd to worktree, git fetch origin, git rebase origin/main, resolve conflicts, git rebase --continue, git push --force-with-lease
+     - Only after resolving conflicts (mergeable: true) can you ask for review"
+        delegator_header="IMPORTANT: Follow the workflow below as your guideline, but prioritize the delegator's message.
 
-IMPORTANT: Follow the workflow below as your guideline, but prioritize the delegator's message.
-
-Workflow:
-1. Read the issue at $instance/$owner/$repo/issues/$number AND all comments on that issue
-2. Check if a PR already exists for this issue
-   - If PR exists and is open, review it and learn from it
-   - If PR makes sense to continue, work on it instead
-   - If PR is not worth continuing, create a new branch/PR but explain in PR description why you're creating a new one instead of continuing the existing PR
-3. Read README.md (if exists) to understand the general concept of this repository
-4. Read CONTRIBUTING.md (if exists) to understand how to contribute
-   - If CONTRIBUTING.md doesn't exist, follow steps 5-9 as your guideline
-5. Explore the repository to understand the codebase
-6. If anything is unclear, post a comment on the issue asking for clarification before implementing
-7. Implement the solution
-8. Create a branch named fix/issue-$number and implement the fix
-9. Create a PR when the implementation is complete using: tea pr create --repo $owner/$repo --title "Your PR title" --body "PR description"
-   - Make sure you are logged in with: tea login add --name gitea --token \$GITEA_TOKEN --url https://$instance
-   - If tea is not available, use: curl -X POST "https://$instance/api/v1/repos/$owner/$repo/pulls" -H "Authorization: Bearer \$GITEA_TOKEN" -H "Content-Type: application/json" -d '{"title":"PR Title","head":"branch-name","base":"main","body":"PR description"}'
-
-Tools for PR interaction:
-- Post issue/PR comment: curl -X POST "https://$instance/api/v1/repos/$owner/$repo/issues/$number/comments" -H "Authorization: Bearer \$GITEA_TOKEN" -H "Content-Type: application/json" -d '{"body":"Your comment"}'
-- List PR comments: curl -s "https://$instance/api/v1/repos/$owner/$repo/issues/$number/comments" -H "Authorization: Bearer \$GITEA_TOKEN"
-- List PR reviews: curl -s "https://$instance/api/v1/repos/$owner/$repo/pulls/$number/reviews" -H "Authorization: Bearer \$GITEA_TOKEN"
-- Merge PR (only with approval): tea pr merge --repo $owner/$repo $number --style merge
-  - MERGING requires approval first! Check for: approval in reviews, OR "lgtm"/"approved" in comments
-  - If no approval, ask reviewer to approve first before merging
+Workflow:"
+        delegator_footer="
 
 Delegator's message:
-$user_message
-
-Work directory: $worktree_path
-EOF
+$user_message"
     else
+        review_notes="  - IMPORTANT: After listing reviews, READ the review comments and incorporate feedback
+  - Check for review state: \"APPROVED\" means ready to merge, \"COMMENT\" means feedback to address"
+        delegator_header="Workflow:"
+    fi
+    
     cat <<EOF
 You are assigned to work on $issue_ref.
 
-Workflow:
+$delegator_header
 1. Read the issue at $instance/$owner/$repo/issues/$number AND all comments on that issue
 2. Check if a PR already exists for this issue
    - If PR exists and is open, review it and learn from it
+$conflict_check
    - If PR makes sense to continue, work on it instead
    - If PR is not worth continuing, create a new branch/PR but explain in PR description why you're creating a new one instead of continuing the existing PR
 3. Read README.md (if exists) to understand the general concept of this repository
@@ -331,13 +351,14 @@ Tools for PR interaction:
 - Post issue/PR comment: curl -X POST "https://$instance/api/v1/repos/$owner/$repo/issues/$number/comments" -H "Authorization: Bearer \$GITEA_TOKEN" -H "Content-Type: application/json" -d '{"body":"Your comment"}'
 - List PR comments: curl -s "https://$instance/api/v1/repos/$owner/$repo/issues/$number/comments" -H "Authorization: Bearer \$GITEA_TOKEN"
 - List PR reviews: curl -s "https://$instance/api/v1/repos/$owner/$repo/pulls/$number/reviews" -H "Authorization: Bearer \$GITEA_TOKEN"
+$review_notes
 - Merge PR (only with approval): tea pr merge --repo $owner/$repo $number --style merge
   - MERGING requires approval first! Check for: approval in reviews, OR "lgtm"/"approved" in comments
   - If no approval, ask reviewer to approve first before merging
+$delegator_footer
 
 Work directory: $worktree_path
 EOF
-    fi
 }
 
 ensure_worktree() {
@@ -390,20 +411,20 @@ ensure_session() {
         session_exists=true
     fi
     
-    if $worktree_exists && $session_exists; then
+    if [ "$worktree_exists" = true ] && [ "$session_exists" = true ]; then
         log "info" "ensure_session" "Session already exists for $issue_ref"
         echo "continued"
         return 0
     fi
     
-    if ! $worktree_exists && $session_exists; then
+    if [ "$worktree_exists" = false ] && [ "$session_exists" = true ]; then
         log "warn" "ensure_session" "Session exists but worktree is missing. Removing stale session..."
         rm -f "$session_path"
         remove_issue_from_index "$issue_ref"
         session_exists=false
     fi
     
-    if ! $worktree_exists; then
+    if [ "$worktree_exists" = false ]; then
         local wt_status=$(ensure_worktree "$issue_ref")
         if [ "$wt_status" != "created" ] && [ "$wt_status" != "existed" ]; then
             log "error" "ensure_session" "Failed to ensure worktree for $issue_ref"

skills/kugetsu/scripts/kugetsu-worktree.sh

@@ -76,7 +76,8 @@ create_worktree() {
         exit 1
     fi
     
-    local worktree_parent_dir=$(dirname "$worktree_path")
+    local worktree_parent_dir
+    worktree_parent_dir=$(dirname "$worktree_path")
     mkdir -p "$worktree_parent_dir"
     
     if worktree_exists "$issue_ref" "$parent_dir"; then
@@ -85,15 +86,36 @@ create_worktree() {
     fi
     
     echo "Creating worktree at '$worktree_path'..."
-    git clone "$repo_url" "$worktree_path" 2>/dev/null || {
-        echo "Error: Failed to clone repository" >&2
+    
+    local clone_success=false
+    local attempt=0
+    local max_attempts="${NETWORK_RETRY_ATTEMPTS:-3}"
+    
+    while [ $attempt -lt $max_attempts ] && [ "$clone_success" = false ]; do
+        attempt=$((attempt + 1))
+        if [ $attempt -gt 1 ]; then
+            echo "Clone attempt $attempt of $max_attempts..."
+            sleep "$((attempt * 2))"
+        fi
+        
+        if git clone "$repo_url" "$worktree_path" 2>/dev/null; then
+            clone_success=true
+        fi
+    done
+    
+    if [ "$clone_success" = false ]; then
+        echo "Error: Failed to clone repository after $max_attempts attempts" >&2
         exit 1
-    }
+    fi
     
     echo "Creating branch '$branch_name'..."
-    (cd "$worktree_path" && git checkout -b "$branch_name" origin/main 2>/dev/null || git checkout -b "$branch_name" main 2>/dev/null) || {
+    if git -C "$worktree_path" checkout -b "$branch_name" origin/main 2>/dev/null; then
+        :
+    elif git -C "$worktree_path" checkout -b "$branch_name" main 2>/dev/null; then
+        :
+    else
         echo "Warning: Could not checkout branch (may need to run from within worktree after session)" >&2
-    }
+    fi
     
     echo "Worktree created at: $worktree_path"
 }
@@ -145,15 +167,17 @@ check_pr_status() {
         token="${GITEA_TOKEN:-}"
     fi
     
-    local response
+    local response_file="$KUGETSU_DIR/.pr_status_response_$$.json"
     if [ -n "$token" ]; then
-        response=$(curl -s -H "Authorization: token $token" "$api_url" 2>/dev/null || echo "{}")
+        curl -s -H "Authorization: token $token" "$api_url" > "$response_file" 2>/dev/null || printf '{}' > "$response_file"
     else
-        response=$(curl -s "$api_url" 2>/dev/null || echo "{}")
+        curl -s "$api_url" > "$response_file" 2>/dev/null || printf '{}' > "$response_file"
     fi
     
-    local state=$(echo "$response" | python3 -c "import json, sys; d=json.load(sys.stdin); print(d.get('state', 'unknown'))" 2>/dev/null || echo "unknown")
-    local merged=$(echo "$response" | python3 -c "import json, sys; d=json.load(sys.stdin); print('true' if d.get('merged', False) else 'false')" 2>/dev/null || echo "false")
+    local state=$(python3 -c "import json; print(json.load(open('$response_file')).get('state', 'unknown'))" 2>/dev/null || echo "unknown")
+    local merged=$(python3 -c "import json; print('true' if json.load(open('$response_file')).get('merged', False) else 'false')" 2>/dev/null || echo "false")
+    
+    rm -f "$response_file"
     
     if [ "$merged" = "true" ]; then
         echo "merged"