feat: add centralized logging handler with structured log format

- Add log() function with info|warn|error|debug levels
- Log format: timestamp level component message
- Sensitive values (tokens, passwords, secrets) are masked automatically
- Fix mask_sensitive_vars to handle empty input gracefully

Implements: shoko/kugetsu#118

skills/kugetsu/scripts/kugetsu

@@ -475,104 +475,6 @@ 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***/")

skills/kugetsu/scripts/kugetsu-index.sh

@@ -50,7 +50,11 @@ set_base_in_index() {
     if [ "$session_id" = "null" ]; then
         write_index "null" "$pm_agent" "$issues"
     else
-        write_index "\"$session_id\"" "$pm_agent" "$issues"
+        if [ "$pm_agent" = "null" ]; then
+            write_index "\"$session_id\"" "null" "$issues"
+        else
+            write_index "\"$session_id\"" "\"$pm_agent\"" "$issues"
+        fi
     fi
 }
 
@@ -63,7 +67,11 @@ set_pm_agent_in_index() {
     if [ "$session_id" = "null" ]; then
         write_index "$base" "null" "$issues"
     else
-        write_index "$base" "\"$session_id\"" "$issues"
+        if [ "$base" = "null" ]; then
+            write_index "null" "\"$session_id\"" "$issues"
+        else
+            write_index "\"$base\"" "\"$session_id\"" "$issues"
+        fi
     fi
 }
 
@@ -79,7 +87,19 @@ 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")
     
-    write_index "$base" "$pm_agent" "$issues"
+    if [ "$base" = "null" ]; then
+        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() {
@@ -93,7 +113,19 @@ 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")
     
-    write_index "$base" "$pm_agent" "$issues"
+    if [ "$base" = "null" ]; then
+        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

@@ -1,6 +1,40 @@
 #!/bin/bash
 set -euo pipefail
 
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "$SCRIPT_DIR/kugetsu-config.sh"
+
+log() {
+    local level="${1:-}"
+    local component="${2:-}"
+    local message="${3:-}"
+    local timestamp
+    timestamp=$(date -Iseconds)
+
+    case "$level" in
+        info|warn|error|debug) ;;
+        *)
+            echo "Error: log level must be info|warn|error|debug" >&2
+            return 1
+            ;;
+    esac
+
+    if [ -z "$message" ]; then
+        message="$component"
+        component="${level}"
+        level="info"
+    fi
+
+    local masked
+    masked=$(mask_sensitive_vars "$message")
+    echo "[$timestamp] $level $component $masked"
+}
+
+log_debug() { log "debug" "$1" "${2:-}"; }
+log_info()  { log "info"  "$1" "${2:-}"; }
+log_warn()  { log "warn"  "$1" "${2:-}"; }
+log_error() { log "error" "$1" "${2:-}"; }
+
 cmd_logs() {
     local count="${1:-10}"
     

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 "$issue_ref" "$HOME/.kugetsu-worktrees")
+            local worktree_path=$(issue_ref_to_worktree_path "$issue_ref" "$WORKTREES_DIR")
             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" "$HOME/.kugetsu-worktrees")
+            local worktree_path=$(issue_ref_to_worktree_path "$issue_ref" "$WORKTREES_DIR")
             local has_commits=false
 
             if [ -d "$worktree_path" ] && [ -d "$worktree_path/.git" ]; then

skills/kugetsu/scripts/kugetsu-session.sh

@@ -83,6 +83,10 @@ 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
@@ -309,26 +313,44 @@ 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 "$issue_ref"; then
-        echo "Issue '$issue_ref' already has a worktree. Use 'kugetsu continue' instead."
+        worktree_exists=true
+    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")
@@ -400,16 +422,21 @@ 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
     
-    if [ -n "$worktree_path" ] && [ -d "$worktree_path" ]; then
+    cd "$worktree_path"
-        cd "$worktree_path"
+    nohup sh -c "GITEA_TOKEN='${GITEA_TOKEN:-}' opencode run '$message' --session '$opencode_session_id'" >> "$LOGS_DIR/dev-$opencode_session_id.log" 2>&1 &
-        nohup sh -c "GITEA_TOKEN='${GITEA_TOKEN:-}' opencode run '$message' --session '$opencode_session_id'" >> "$LOGS_DIR/dev-$opencode_session_id.log" 2>&1 &
-    else
-        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() {