fix: add JSON validation in write_index to prevent malformed index.json

The index.json was getting corrupted (ending with 'issues: }' instead of 'issues: {}').
Added validation that checks if the JSON is valid before moving the temp file.
If invalid, the write is aborted with an error message showing the problematic values.

skills/kugetsu/scripts/kugetsu

@@ -475,6 +475,104 @@ read_index() {
     fi
 }
 
+write_index() {
+    local base="$1"
+    local pm_agent="$2"
+    local issues_json="$3"
+    local temp_file="$INDEX_FILE.tmp.$$"
+    printf '{"base": %s, "pm_agent": %s, "issues": %s}\n' "$base" "$pm_agent" "$issues_json" > "$temp_file"
+    
+    if ! python3 -c "import json; json.load(open('$temp_file'))" 2>/dev/null; then
+        echo "Error: write_index would create malformed JSON, aborting. base=$base, pm_agent=$pm_agent, issues_json=$issues_json" >&2
+        rm -f "$temp_file"
+        return 1
+    fi
+    
+    mv "$temp_file" "$INDEX_FILE"
+}
+
+get_base_session_id() {
+    local index=$(read_index)
+    echo "$index" | python3 -c "import sys, json; d=json.load(sys.stdin); print(d.get('base') or '')"
+}
+
+get_pm_agent_session_id() {
+    local index=$(read_index)
+    echo "$index" | python3 -c "import sys, json; d=json.load(sys.stdin); print(d.get('pm_agent') or '')"
+}
+
+get_session_for_issue() {
+    local issue_ref="$1"
+    local index=$(read_index)
+    echo "$index" | python3 -c "import sys, json; d=json.load(sys.stdin); print(d['issues'].get('$issue_ref') or '')"
+}
+
+set_base_in_index() {
+    local base_session_id="$1"
+    local pm_agent=$(get_pm_agent_session_id)
+    local issues_json=$(read_index | python3 -c "import sys, json; d=json.load(sys.stdin); print(json.dumps(d['issues']))")
+    if [ -z "$pm_agent" ] || [ "$pm_agent" = "null" ]; then
+        write_index "\"$base_session_id\"" "null" "$issues_json"
+    else
+        write_index "\"$base_session_id\"" "\"$pm_agent\"" "$issues_json"
+    fi
+}
+
+set_pm_agent_in_index() {
+    local pm_agent_session_id="$1"
+    local base=$(get_base_session_id)
+    local issues_json=$(read_index | python3 -c "import sys, json; d=json.load(sys.stdin); print(json.dumps(d['issues']))")
+    if [ -z "$base" ] || [ "$base" = "null" ]; then
+        write_index "null" "\"$pm_agent_session_id\"" "$issues_json"
+    else
+        write_index "\"$base\"" "\"$pm_agent_session_id\"" "$issues_json"
+    fi
+}
+
+add_issue_to_index() {
+    local issue_ref="$1"
+    local session_file="$2"
+    local index=$(read_index)
+    local base=$(get_base_session_id)
+    local pm_agent=$(get_pm_agent_session_id)
+    local issues=$(echo "$index" | python3 -c "import sys, json; d=json.load(sys.stdin); print(json.dumps(d['issues']))")
+    local new_issues=$(echo "$issues" | python3 -c "import sys, json; d=json.load(sys.stdin); d['$issue_ref']='$session_file'; print(json.dumps(d))")
+    if [ -z "$base" ] || [ "$base" = "null" ]; then
+        if [ -z "$pm_agent" ] || [ "$pm_agent" = "null" ]; then
+            write_index "null" "null" "$new_issues"
+        else
+            write_index "null" "\"$pm_agent\"" "$new_issues"
+        fi
+    else
+        if [ -z "$pm_agent" ] || [ "$pm_agent" = "null" ]; then
+            write_index "\"$base\"" "null" "$new_issues"
+        else
+            write_index "\"$base\"" "\"$pm_agent\"" "$new_issues"
+        fi
+    fi
+}
+
+remove_issue_from_index() {
+    local issue_ref="$1"
+    local index=$(read_index)
+    local base=$(get_base_session_id)
+    local pm_agent=$(get_pm_agent_session_id)
+    local new_issues=$(echo "$index" | python3 -c "import sys, json; d=json.load(sys.stdin); d['issues'].pop('$issue_ref', None); print(json.dumps(d['issues']))")
+    if [ -z "$base" ] || [ "$base" = "null" ]; then
+        if [ -z "$pm_agent" ] || [ "$pm_agent" = "null" ]; then
+            write_index "null" "null" "$new_issues"
+        else
+            write_index "null" "\"$pm_agent\"" "$new_issues"
+        fi
+    else
+        if [ -z "$pm_agent" ] || [ "$pm_agent" = "null" ]; then
+            write_index "\"$base\"" "null" "$new_issues"
+        else
+            write_index "\"$base\"" "\"$pm_agent\"" "$new_issues"
+        fi
+    fi
+}
+
 validate_issue_ref() {
     local issue_ref="$1"
     if [[ ! "$issue_ref" =~ ^[^/]+/[^/]+/[^#]+#[0-9]+$ ]]; then

skills/kugetsu/scripts/kugetsu-config.sh

@@ -32,7 +32,7 @@ if [ -f "$KUGETSU_DIR/config" ]; then
 fi
 
 mask_sensitive_vars() {
-    local line="${1:-}"
+    local line="$1"
     for var in GITEA_TOKEN GITHUB_TOKEN GITLAB_TOKEN API_KEY PASSWORD TOKEN SECRET; do
         if [[ "$line" =~ $var ]]; then
             line=$(echo "$line" | sed -E "s/=.*/=***MASKED***/")
@@ -41,11 +41,6 @@ mask_sensitive_vars() {
     echo "$line"
 }
 
-strip_ansi_codes() {
-    local line="${1:-}"
-    echo "$line" | sed 's/\x1b\[[0-9;]*m//g' | sed 's/\x1b\[[0-9;]*[a-zA-Z]//g'
-}
-
 load_agent_env() {
     local agent_type="${1:-base}"
     local env_file="$ENV_DIR/${agent_type}.env"
@@ -64,26 +59,3 @@ load_agent_env() {
         set +a
     fi
 }
-
-set_debug_mode() {
-    local filtered_args=()
-    local debug_mode=false
-    
-    for arg in "$@"; do
-        case "$arg" in
-            --debug)
-                debug_mode=true
-                ;;
-            *)
-                filtered_args+=("$arg")
-                ;;
-        esac
-    done
-    
-    if [ "$debug_mode" = true ]; then
-        export KUGETSU_VERBOSITY="debug"
-        echo "[DEBUG] Debug mode enabled" >&2
-    fi
-    
-    echo "${filtered_args[@]}"
-}

skills/kugetsu/scripts/kugetsu-index.sh

@@ -50,11 +50,7 @@ set_base_in_index() {
     if [ "$session_id" = "null" ]; then
         write_index "null" "$pm_agent" "$issues"
     else
-        if [ "$pm_agent" = "null" ]; then
+        write_index "\"$session_id\"" "$pm_agent" "$issues"
-            write_index "\"$session_id\"" "null" "$issues"
-        else
-            write_index "\"$session_id\"" "\"$pm_agent\"" "$issues"
-        fi
     fi
 }
 
@@ -67,11 +63,7 @@ set_pm_agent_in_index() {
     if [ "$session_id" = "null" ]; then
         write_index "$base" "null" "$issues"
     else
-        if [ "$base" = "null" ]; then
+        write_index "$base" "\"$session_id\"" "$issues"
-            write_index "null" "\"$session_id\"" "$issues"
-        else
-            write_index "\"$base\"" "\"$session_id\"" "$issues"
-        fi
     fi
 }
 
@@ -87,19 +79,7 @@ add_issue_to_index() {
     
     issues=$(python3 -c "import sys, json; d=json.load(sys.stdin); d['$issue_ref']='$session_file'; print(json.dumps(d))" <<< "$issues")
     
-    if [ "$base" = "null" ]; then
+    write_index "$base" "$pm_agent" "$issues"
-        if [ "$pm_agent" = "null" ]; then
-            write_index "null" "null" "$issues"
-        else
-            write_index "null" "\"$pm_agent\"" "$issues"
-        fi
-    else
-        if [ "$pm_agent" = "null" ]; then
-            write_index "\"$base\"" "null" "$issues"
-        else
-            write_index "\"$base\"" "\"$pm_agent\"" "$issues"
-        fi
-    fi
 }
 
 remove_issue_from_index() {
@@ -113,19 +93,7 @@ remove_issue_from_index() {
     
     issues=$(python3 -c "import sys, json; d=json.load(sys.stdin); d.pop('$issue_ref', None); print(json.dumps(d))" <<< "$issues")
     
-    if [ "$base" = "null" ]; then
+    write_index "$base" "$pm_agent" "$issues"
-        if [ "$pm_agent" = "null" ]; then
-            write_index "null" "null" "$issues"
-        else
-            write_index "null" "\"$pm_agent\"" "$issues"
-        fi
-    else
-        if [ "$pm_agent" = "null" ]; then
-            write_index "\"$base\"" "null" "$issues"
-        else
-            write_index "\"$base\"" "\"$pm_agent\"" "$issues"
-        fi
-    fi
 }
 
 validate_issue_ref() {

skills/kugetsu/scripts/kugetsu-log.sh

@@ -24,9 +24,7 @@ cmd_logs() {
             echo ""
             echo "--- $log ---"
             tail -20 "$LOGS_DIR/$log" | while read line; do
-                line=$(strip_ansi_codes "$line")
+                echo "  $(mask_sensitive_vars "$line")"
-                line=$(mask_sensitive_vars "$line")
-                echo "  $line"
             done
         fi
     done

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

@@ -44,7 +44,7 @@ check_task_completion() {
 
     if [ -n "$pid" ] && [ "$pid" != "None" ]; then
         if ! kill -0 "$pid" 2>/dev/null; then
-            local worktree_path=$(issue_ref_to_worktree_path "$issue_ref" "$WORKTREES_DIR")
+            local worktree_path=$(issue_ref_to_worktree_path "$issue_ref" "$HOME/.kugetsu-worktrees")
             local has_commits=false
 
             if [ -d "$worktree_path" ] && [ -d "$worktree_path/.git" ]; then
@@ -64,7 +64,7 @@ check_task_completion() {
         fi
     else
         if [ -n "$session_id" ] && ! opencode session list 2>/dev/null | grep -q "$session_id"; then
-            local worktree_path=$(issue_ref_to_worktree_path "$issue_ref" "$WORKTREES_DIR")
+            local worktree_path=$(issue_ref_to_worktree_path "$issue_ref" "$HOME/.kugetsu-worktrees")
             local has_commits=false
 
             if [ -d "$worktree_path" ] && [ -d "$worktree_path/.git" ]; then

skills/kugetsu/scripts/kugetsu-session.sh

@@ -83,10 +83,6 @@ EOF
     if [ -n "$existing_base" ] && [ "$existing_base" != "null" ]; then
         if [ "$force" = true ]; then
             echo "Warning: Reinitializing sessions (force mode)" >&2
-            echo "Destroying all sessions, worktrees, and logs..." >&2
-            cmd_destroy --base -y 2>/dev/null || true
-            cmd_destroy --pm-agent -y 2>/dev/null || true
-            rm -f "$LOGS_DIR"/*.log 2>/dev/null || true
         else
             echo "Error: Base session already exists: $existing_base" >&2
             echo "Use --force to reinitialize" >&2
@@ -225,9 +221,7 @@ cmd_delegate() {
         exit 1
     fi
     
-    local msg_file="$LOGS_DIR/msg-$new_session.txt"
+    nohup sh -c "GITEA_TOKEN='${GITEA_TOKEN:-}' opencode run '$message' --session '$new_session'" >> "$log_file" 2>&1 &
-    printf '%s' "$message" > "$msg_file"
-    nohup sh -c "GITEA_TOKEN='${GITEA_TOKEN:-}' opencode run '@$msg_file' --session '$new_session'" >> "$log_file" 2>&1 &
     echo "Delegated to new session (logged to $(basename "$log_file"))"
 }
 
@@ -240,22 +234,20 @@ create_session() {
     fi
     
     local before_json=$(opencode session list --format=json 2>/dev/null)
-    local before_set=$(echo "$before_json" | python3 -c "import sys,json; sessions=json.load(sys.stdin); print('|'.join(s['id'] for s in sessions))" 2>/dev/null || echo "|")
+    local before_ids=$(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 "")
     
-    opencode run --fork --session "$base_session" "new session" >/dev/null 2>&1
+    opencode run --fork --session "$base_session" "new session" 2>/dev/null
-    
-    sleep 1
     
     local after_json=$(opencode session list --format=json 2>/dev/null)
-    local after_sessions=$(echo "$after_json" | python3 -c "import sys,json; sessions=json.load(sys.stdin); [print(s['id']) for s in sessions]" 2>/dev/null || true)
+    local after_ids=$(echo "$after_json" | python3 -c "import sys,json; sessions=json.load(sys.stdin); print(' '.join(s['id'] for s in sessions))" 2>/dev/null || echo "")
     
     local new_session_id=""
-    while IFS= read -r sess; do
+    for sess in $after_ids; do
-        if [[ -n "$sess" ]] && [[ ! "$before_set" =~ \|${sess}\| ]]; then
+        if [[ ! " $before_ids " =~ " $sess " ]] && [[ "$sess" != "$base_session" ]]; then
             new_session_id="$sess"
             break
         fi
-    done <<< "$after_sessions"
+    done
     
     echo "$new_session_id"
 }
@@ -317,44 +309,26 @@ cmd_start() {
         exit 1
     fi
     
-    local session_file=$(issue_ref_to_filename "$issue_ref")
-    local session_path="$SESSIONS_DIR/$session_file"
-    local worktree_exists=false
-    
     if worktree_exists "$issue_ref"; then
-        worktree_exists=true
+        echo "Issue '$issue_ref' already has a worktree. Use 'kugetsu continue' instead."
-    fi
-    
-    local session_exists=false
-    if [ -f "$session_path" ]; then
-        session_exists=true
-    fi
-    
-    if $worktree_exists && $session_exists; then
-        echo "Issue '$issue_ref' already has a worktree and session." >&2
-        echo "Use 'kugetsu continue $issue_ref' to continue work." >&2
         exit 1
     fi
     
-    if $worktree_exists && ! $session_exists; then
-        echo "Warning: Worktree exists but session is missing. Removing worktree to recreate both..." >&2
-        remove_worktree_for_issue "$issue_ref"
-        worktree_exists=false
-    fi
-    
-    if ! $worktree_exists && $session_exists; then
-        echo "Warning: Session exists but worktree is missing. Removing stale session to recreate both..." >&2
-        rm -f "$session_path"
-        remove_issue_from_index "$issue_ref"
-        session_exists=false
-    fi
-    
     local active_count=$(count_active_dev_sessions)
     if [ "$active_count" -ge "${MAX_CONCURRENT_AGENTS:-3}" ]; then
         echo "Error: Max concurrent agents (${MAX_CONCURRENT_AGENTS:-3}) reached. Use 'kugetsu continue' or wait for an agent to finish." >&2
         exit 1
     fi
     
+    local session_file=$(issue_ref_to_filename "$issue_ref")
+    local session_path="$SESSIONS_DIR/$session_file"
+    
+    if [ -f "$session_path" ]; then
+        echo "Session file already exists: $session_file"
+        echo "Use 'kugetsu continue $issue_ref' to continue work."
+        exit 1
+    fi
+    
     create_worktree "$issue_ref" "$WORKTREES_DIR"
     
     local new_session_id=$(create_session "$base_session_id")
@@ -377,10 +351,7 @@ cmd_start() {
     load_agent_env "dev"
     
     cd "$worktree_path"
-    local sanitized_id=$(echo "$new_session_id" | sed 's/[^a-zA-Z0-9_-]/_/g')
+    nohup sh -c "GITEA_TOKEN='${GITEA_TOKEN:-}' opencode run '$dev_message' --session '$new_session_id'" >> "$LOGS_DIR/dev-$new_session_id.log" 2>&1 &
-    local msg_file="$worktree_path/.kugetsu-msg.txt"
-    printf '%s' "$dev_message" > "$msg_file"
-    nohup sh -c "GITEA_TOKEN='${GITEA_TOKEN:-}' opencode run '@$msg_file' --session '$new_session_id'" >> "$LOGS_DIR/dev-$sanitized_id.log" 2>&1 &
     
     echo "Session started for '$issue_ref': $new_session_id"
     echo "Worktree: $worktree_path"
@@ -429,24 +400,16 @@ cmd_continue() {
     local worktree_path=$(python3 -c "import json; print(json.load(open('$session_path')).get('worktree_path', ''))" 2>/dev/null || echo "")
     local issue_ref=$(python3 -c "import json; print(json.load(open('$session_path')).get('issue_ref', ''))" 2>/dev/null || echo "")
     
-    if [ -z "$worktree_path" ] || [ ! -d "$worktree_path" ]; then
-        echo "Warning: Worktree is missing for '$session_name'. Recovering..." >&2
-        rm -f "$session_path"
-        remove_issue_from_index "$session_name"
-        echo "Calling cmd_start to create new session and worktree..." >&2
-        cmd_start "$session_name" "$message"
-        return $?
-    fi
-    
     if [ -z "$message" ]; then
         message=$(build_dev_agent_message "$issue_ref" "")
     fi
     
-    cd "$worktree_path"
+    if [ -n "$worktree_path" ] && [ -d "$worktree_path" ]; then
-    local sanitized_id=$(echo "$opencode_session_id" | sed 's/[^a-zA-Z0-9_-]/_/g')
+        cd "$worktree_path"
-    local msg_file="$worktree_path/.kugetsu-msg.txt"
+        nohup sh -c "GITEA_TOKEN='${GITEA_TOKEN:-}' opencode run '$message' --session '$opencode_session_id'" >> "$LOGS_DIR/dev-$opencode_session_id.log" 2>&1 &
-    printf '%s' "$message" > "$msg_file"
+    else
-    nohup sh -c "GITEA_TOKEN='${GITEA_TOKEN:-}' opencode run '@$msg_file' --session '$opencode_session_id'" >> "$LOGS_DIR/dev-$sanitized_id.log" 2>&1 &
+        nohup sh -c "GITEA_TOKEN='${GITEA_TOKEN:-}' opencode run '$message' --session '$opencode_session_id'" >> "$LOGS_DIR/dev-$opencode_session_id.log" 2>&1 &
+    fi
 }
 
 cmd_list() {