fix(worktree-lifecycle): use github.com as example in set-pr help

- Remove accidentally committed worktree directory

skills/kugetsu/scripts/kugetsu

@@ -13,6 +13,7 @@ VERBOSITY_DIR="$KUGETSU_DIR/verbosity"
 
 MAX_CONCURRENT_AGENTS="${MAX_CONCURRENT_AGENTS:-3}"
 KUGETSU_VERBOSITY="${KUGETSU_VERBOSITY:-default}"
+WORKTREE_CHECK_PR_STATUS="${WORKTREE_CHECK_PR_STATUS:-true}"
 
 # Load user config overrides (~/.kugetsu/config)
 if [ -f "$KUGETSU_DIR/config" ]; then
@@ -76,7 +77,8 @@ Usage:
     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 destroy --base [-y]                      Delete base session
+    kugetsu set-pr <issue-ref> <pr-url>            Set PR URL for session (for PR tracking)
     kugetsu help                                     Show this help
 
 Issue Ref Format:
@@ -256,6 +258,54 @@ get_worktree_path_for_session() {
     fi
 }
 
+check_pr_status() {
+    local pr_url="$1"
+    
+    if [ -z "$pr_url" ]; then
+        echo "no_pr_url"
+        return 1
+    fi
+    
+    local hostname=$(echo "$pr_url" | sed -E 's|https://([^/]+)/.*|\1|')
+    
+    local server_base="${GIT_SERVERS[$hostname]:-}"
+    if [ -z "$server_base" ]; then
+        echo "unknown_server"
+        return 1
+    fi
+    
+    local api_base="${server_base}/api/v1"
+    
+    local api_url=$(echo "$pr_url" | sed -E 's|https://[^/]+/([^/]+)/([^/]+)/(pulls|merge_requests)/([0-9]+)|'"${api_base}"'/repos/\1/\2/\3/\4|')
+    
+    local token=""
+    if [[ "$hostname" == "github.com" ]]; then
+        token="${GITHUB_TOKEN:-}"
+    else
+        token="${GITEA_TOKEN:-}"
+    fi
+    
+    local response
+    if [ -n "$token" ]; then
+        response=$(curl -s -H "Authorization: token $token" "$api_url" 2>/dev/null || echo "{}")
+    else
+        response=$(curl -s "$api_url" 2>/dev/null || echo "{}")
+    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")
+    
+    if [ "$merged" = "true" ]; then
+        echo "merged"
+    elif [ "$state" = "closed" ]; then
+        echo "closed"
+    elif [ "$state" = "open" ]; then
+        echo "open"
+    else
+        echo "unknown"
+    fi
+}
+
 issue_ref_to_filename() {
     local issue_ref="$1"
     echo "$issue_ref" | sed 's/[\/:]/-/g' | sed 's/#/-/'
@@ -267,6 +317,46 @@ filename_to_issue_ref() {
     echo "$name" | sed 's/-\([0-9]*\)$/#\1' | sed 's/-/\//g'
 }
 
+update_session_pr_url() {
+    local issue_ref="$1"
+    local pr_url="$2"
+    
+    if [ -z "$issue_ref" ] || [ -z "$pr_url" ]; then
+        echo "Error: update_session_pr_url requires <issue-ref> and <pr-url>" >&2
+        return 1
+    fi
+    
+    local session_file=$(get_session_for_issue "$issue_ref")
+    if [ -z "$session_file" ] || [ "$session_file" = "null" ]; then
+        echo "Error: No session found for '$issue_ref'" >&2
+        return 1
+    fi
+    
+    local session_path="$SESSIONS_DIR/$session_file"
+    
+    if [ ! -f "$session_path" ]; then
+        echo "Error: Session file not found: $session_path" >&2
+        return 1
+    fi
+    
+    python3 << PYEOF
+import json
+
+session_path = "$session_path"
+pr_url = "$pr_url"
+
+with open(session_path, 'r') as f:
+    session = json.load(f)
+
+session['pr_url'] = pr_url
+
+with open(session_path, 'w') as f:
+    json.dump(session, f, indent=2)
+
+print(f"Updated pr_url to: {pr_url}")
+PYEOF
+}
+
 read_index() {
     if [ -f "$INDEX_FILE" ]; then
         cat "$INDEX_FILE"
@@ -394,6 +484,41 @@ kugetsu_get_pm_context() {
     fi
 }
 
+kugetsu_get_fork_context() {
+    local issue_ref="$1"
+    local context=""
+    
+    context="## IMPORTANT WORKING RULES
+
+1. You are working on issue: $issue_ref
+2. If you encounter ANY error, blocker, or cannot complete the task:
+   - STOP immediately
+   - Log what happened and why you cannot proceed
+   - Do NOT switch to other work or try alternative approaches
+3. Do NOT work on other issues or PRs unless explicitly asked
+4. Environment variables are available in ~/.kugetsu/env/
+
+"
+    
+    if [ -f "$REPOS_CONFIG" ]; then
+        context="${context}
+## REPOSITORIES CONFIG
+$(cat "$REPOS_CONFIG")
+
+"
+    fi
+    
+    if [ -f "$ENV_DIR/default.env" ]; then
+        context="${context}
+## ENVIRONMENT (available at ~/.kugetsu/env/)
+Environment file exists at: $ENV_DIR/default.env
+Source it with: source ~/.kugetsu/env/default.env
+"
+    fi
+    
+    echo "$context"
+}
+
 kugetsu_add_notification() {
     local type="$1"
     local message="$2"
@@ -606,6 +731,99 @@ EOF
     fi
 }
 
+parse_issue_ref_from_message() {
+    local message="$1"
+    
+    local gitserver=""
+    local owner=""
+    local repo=""
+    local issue_number=""
+    
+    if echo "$message" | grep -qE '[a-zA-Z0-9.-]+\.[a-zA-Z]{2,}/[a-zA-Z0-9_.-]+/[a-zA-Z0-9_.-]+/(issues|pull)/[0-9]+'; then
+        gitserver=$(echo "$message" | grep -oE '[a-zA-Z0-9.-]+\.[a-zA-Z]{2,}/[a-zA-Z0-9_.-]+/[a-zA-Z0-9_.-]+' | head -1 | sed 's/\/[^/]*\/[^/]*$//')
+        local full_path=$(echo "$message" | grep -oE '[a-zA-Z0-9.-]+\.[a-zA-Z]{2,}/[a-zA-Z0-9_.-]+/[a-zA-Z0-9_.-]+/(issues|pull)/[0-9]+' | head -1)
+        owner=$(echo "$full_path" | cut -d'/' -f2)
+        repo=$(echo "$full_path" | cut -d'/' -f3)
+        issue_number=$(echo "$full_path" | grep -oE '[0-9]+$' | head -1)
+    elif echo "$message" | grep -qE '[a-zA-Z0-9_.-]+/[a-zA-Z0-9_.-]+#([0-9]+)'; then
+        owner=$(echo "$message" | grep -oE '[a-zA-Z0-9_.-]+/[a-zA-Z0-9_.-]+#' | sed 's/#$//' | cut -d'/' -f1)
+        repo=$(echo "$message" | grep -oE '[a-zA-Z0-9_.-]+/[a-zA-Z0-9_.-]+#' | sed 's/#$//' | cut -d'/' -f2)
+        issue_number=$(echo "$message" | grep -oE '#[0-9]+' | grep -oE '[0-9]+' | head -1)
+    fi
+    
+    echo "${gitserver}|${owner}|${repo}|${issue_number}"
+}
+
+get_missing_info() {
+    local parsed="$1"
+    local gitserver=$(echo "$parsed" | cut -d'|' -f1)
+    local owner=$(echo "$parsed" | cut -d'|' -f2)
+    local repo=$(echo "$parsed" | cut -d'|' -f3)
+    local issue_number=$(echo "$parsed" | cut -d'|' -f4)
+    
+    local missing=""
+    [ -z "$gitserver" ] && missing="${missing}git server, "
+    [ -z "$owner" ] && missing="${missing}owner, "
+    [ -z "$repo" ] && missing="${missing}repository, "
+    [ -z "$issue_number" ] && missing="${missing}issue number, "
+    
+    echo "$missing" | sed 's/, $//'
+}
+
+build_missing_info_context() {
+    local missing="$1"
+    if [ -n "$missing" ]; then
+        echo ""
+        echo "NOTE: This task delegation has no information about: ${missing}."
+        echo "We need them if user wants to work on a specific issue. Otherwise we don't need it."
+    fi
+}
+
+find_worktrees_by_issue_number() {
+    local issue_number="$1"
+    local results=""
+    
+    if [ ! -d "$WORKTREES_DIR/.kugetsu-worktrees" ]; then
+        echo ""
+        return
+    fi
+    
+    for wt in "$WORKTREES_DIR/.kugetsu-worktrees"/*; do
+        if [ -d "$wt" ]; then
+            local wt_issue_number=$(echo "$wt" | grep -oE '#?[0-9]+$' | grep -oE '[0-9]+' | head -1)
+            if [ "$wt_issue_number" = "$issue_number" ]; then
+                results="${results}${wt}:worktree
+"
+            fi
+        fi
+    done
+    
+    echo "$results"
+}
+
+find_sessions_by_issue_number() {
+    local issue_number="$1"
+    local results=""
+    
+    if [ ! -d "$SESSIONS_DIR" ]; then
+        echo ""
+        return
+    fi
+    
+    for session_file in "$SESSIONS_DIR"/*.json; do
+        if [ -f "$session_file" ]; then
+            local session_issue_ref=$(basename "$session_file" .json | sed 's/_/\//g')
+            local session_issue_number=$(echo "$session_issue_ref" | grep -oE '#?[0-9]+$' | grep -oE '[0-9]+' | head -1)
+            if [ "$session_issue_number" = "$issue_number" ]; then
+                results="${results}${session_file}:session
+"
+            fi
+        fi
+    done
+    
+    echo "$results"
+}
+
 cmd_delegate() {
     local message="${1:-}"
     local verbosity="${KUGETSU_VERBOSITY:-default}"
@@ -625,6 +843,70 @@ cmd_delegate() {
     mkdir -p "$LOGS_DIR"
     local log_file="$LOGS_DIR/delegate-$(date +%s).log"
     
+    local parsed=$(parse_issue_ref_from_message "$message")
+    local gitserver=$(echo "$parsed" | cut -d'|' -f1)
+    local owner=$(echo "$parsed" | cut -d'|' -f2)
+    local repo=$(echo "$parsed" | cut -d'|' -f3)
+    local issue_number=$(echo "$parsed" | cut -d'|' -f4)
+    
+    local missing_info=$(get_missing_info "$parsed")
+    local context_injection=""
+    if [ -n "$missing_info" ]; then
+        context_injection=$(build_missing_info_context "$missing_info")
+        echo "NOTE: Delegation missing information: ${missing_info}"
+    fi
+    
+    local candidates=""
+    local candidate_count=0
+    
+    if [ -n "$issue_number" ]; then
+        local worktrees=$(find_worktrees_by_issue_number "$issue_number")
+        local sessions=$(find_sessions_by_issue_number "$issue_number")
+        
+        while IFS=: read -r path type; do
+            if [ -n "$path" ]; then
+                candidate_count=$((candidate_count + 1))
+                candidates="${candidates}${candidate_count}) ${path} (${type})
+"
+            fi
+        done <<< "$worktrees"
+        
+        while IFS=: read -r path type; do
+            if [ -n "$path" ]; then
+                candidate_count=$((candidate_count + 1))
+                candidates="${candidates}${candidate_count}) ${path} (${type})
+"
+            fi
+        done <<< "$sessions"
+    fi
+    
+    local use_worktree=""
+    if [ $candidate_count -gt 0 ]; then
+        echo "Found $candidate_count existing worktree(s)/session(s) for issue #${issue_number}:"
+        echo "$candidates"
+        echo "r) Delegate anyway (without routing)"
+        echo "Which one to use? [1-${candidate_count}/r]: "
+        read -r choice
+        
+        if [ "$choice" = "r" ] || [ -z "$choice" ]; then
+            use_worktree=""
+        elif [ "$choice" -ge 1 ] && [ "$choice" -le "$candidate_count" ]; then
+            local selected=$(echo "$candidates" | sed -n "${choice}p")
+            use_worktree=$(echo "$selected" | sed 's/) .*//')
+        fi
+    fi
+    
+    local final_message="${message}${context_injection}"
+    
+    if [ -n "$use_worktree" ]; then
+        if [ -d "$use_worktree" ]; then
+            echo "Using worktree: $use_worktree"
+            final_message="${final_message}
+
+NOTE: Worktree selected: ${use_worktree}"
+        fi
+    fi
+    
     local temp_dir="${KUGETSU_TEMP_DIR:-$HOME/.local/share/opencode/tool-output}"
     
     mkdir -p "$ENV_DIR"
@@ -636,7 +918,7 @@ cmd_delegate() {
     fi
     env_sh="${env_sh}set +a; "
     
-    nohup sh -c "${env_sh}opencode run '$message' --continue --session '$pm_session' >> '$log_file' 2>&1" > /dev/null 2>&1 &
+    nohup sh -c "${env_sh}opencode run '${final_message}' --continue --session '$pm_session' >> '$log_file' 2>&1" > /dev/null 2>&1 &
     disown
     echo "Delegated to PM agent (logged to $(basename "$log_file"))"
     echo "Verbosity: $verbosity"
@@ -876,7 +1158,7 @@ cmd_doctor() {
 }
 
 fix_session_permissions() {
-    local opencode_db="${OPENCODE_DB:-$HOME/.opencode/opencode.db}"
+    local opencode_db="${OPENCODE_DB:-$HOME/.local/share/opencode/opencode.db}"
     
     if [ ! -f "$opencode_db" ]; then
         echo "[ERROR] opencode database not found: $opencode_db"
@@ -1088,6 +1370,11 @@ EOF
         echo "Created pm-agent env file: $ENV_DIR/pm-agent.env"
     fi
 
+    if [ -d "$LOGS_DIR" ]; then
+        echo "Cleaning up old logs..."
+        rm -rf "$LOGS_DIR"/*.log 2>/dev/null || true
+    fi
+
     local existing_base=$(get_base_session_id)
     local existing_pm=$(get_pm_agent_session_id)
     
@@ -1107,6 +1394,29 @@ EOF
         exit 1
     fi
 
+    local init_worktree_dir="$HOME/.kugetsu-worktrees"
+    mkdir -p "$init_worktree_dir"
+    cd "$init_worktree_dir"
+    echo "Initialized kugetsu worktrees directory: $init_worktree_dir"
+    echo "Base session will be created in this directory."
+    echo ""
+
+    local cwd_files=$(ls -A "$PWD" 2>/dev/null | wc -l)
+    local cwd_git=$(git rev-parse --is-inside-work-tree 2>/dev/null || echo "false")
+    if [ "$cwd_files" -gt 0 ] || [ "$cwd_git" = "true" ]; then
+        echo "Warning: Worktrees directory is not empty: $PWD" >&2
+        echo "This may cause project context to contaminate the base session." >&2
+        echo "Consider running kugetsu destroy --base -y and reinitializing." >&2
+        echo "" >&2
+        echo "Files in current directory: $cwd_files" >&2
+        if [ "$cwd_git" = "true" ]; then
+            echo "Git repository detected: $(git rev-parse --show-toplevel 2>/dev/null || echo 'unknown')" >&2
+        fi
+        echo "" >&2
+        echo "Press Ctrl+C to cancel or wait 5 seconds to continue anyway..." >&2
+        sleep 5
+    fi
+
     echo "Starting TUI to create base session..."
     echo "Press Ctrl+C to cancel or wait for session to be created"
     sleep 2
@@ -1181,6 +1491,7 @@ EOF
 cmd_start() {
     local issue_ref=""
     local message=""
+    local pr_url=""
     local args=("$@")
 
     args=$(set_debug_mode "${args[@]}")
@@ -1190,11 +1501,14 @@ cmd_start() {
             issue_ref="$arg"
         elif [ -z "$message" ]; then
             message="$arg"
+        elif [ -z "$pr_url" ]; then
+            pr_url="$arg"
         fi
     done
 
     if [ -z "$issue_ref" ] || [ -z "$message" ]; then
         echo "Error: start requires <issue-ref> and <message>" >&2
+        echo "Usage: kugetsu start <issue-ref> <message> [pr-url]" >&2
         exit 1
     fi
 
@@ -1226,12 +1540,6 @@ cmd_start() {
 
     local session_file="$(issue_ref_to_filename "$issue_ref").json"
 
-    # Get list of sessions before fork to compare against after
-    declare -a before_sessions=()
-    while IFS= read -r sess; do
-        before_sessions+=("$sess")
-    done < <(opencode session list 2>/dev/null | grep -oP '^ses_\w+')
-
     echo "Forking session for '$issue_ref'..."
     
     # Session-counting: count actual dev sessions, reject if at limit
@@ -1242,16 +1550,24 @@ cmd_start() {
         remove_worktree_for_issue "$issue_ref" "$parent_dir"
         exit 1
     fi
-    
+     
     local fork_log="$SESSIONS_DIR/$session_file.fork.log"
     local opencode_db="${OPENCODE_DB:-$HOME/.local/share/opencode/opencode.db}"
     
+    > "$fork_log"
+    
+    local fork_context=$(kugetsu_get_fork_context "$issue_ref")
+    local full_message="${fork_context}
+
+## YOUR TASK
+$message"
+    
     fix_session_permissions
     
     if [ "$DEBUG_MODE" = true ]; then
-        (cd "$worktree_path" && opencode run "$message" --fork --session "$base_session_id" 2>&1) | tee "$fork_log" &
+        (cd "$worktree_path" && opencode run "$full_message" --fork --session "$base_session_id" --dir "$worktree_path" 2>&1) | tee "$fork_log" &
     else
-        (cd "$worktree_path" && opencode run "$message" --fork --session "$base_session_id" 2>&1) >> "$fork_log" &
+        (cd "$worktree_path" && opencode run "$full_message" --fork --session "$base_session_id" --dir "$worktree_path" 2>&1) >> "$fork_log" &
     fi
 
     local fork_pid=$!
@@ -1264,25 +1580,17 @@ cmd_start() {
     while [ $attempt -le $max_attempts ]; do
         sleep 1
         
-        while IFS= read -r sess; do
-            [ "$sess" = "$base_session_id" ] && continue
-            [ "$sess" = "$pm_agent_session_id" ] && continue
-            
-            local existed_before=false
-            for before_sess in "${before_sessions[@]}"; do
-                if [ "$sess" = "$before_sess" ]; then
-                    existed_before=true
-                    break
-                fi
-            done
-            
-            if [ "$existed_before" = false ]; then
-                new_session_id="$sess"
-                break
-            fi
-        done < <(opencode session list 2>/dev/null | grep -oP '^ses_\w+')
+        new_session_id=$(python3 -c "
+import sqlite3
+conn = sqlite3.connect('$opencode_db')
+cursor = conn.cursor()
+cursor.execute(\"SELECT id FROM session WHERE directory = '$worktree_path' ORDER BY time_created DESC LIMIT 1\")
+result = cursor.fetchone()
+if result:
+    print(result[0])
+" 2>/dev/null || echo "")
         
-        if [ -n "$new_session_id" ]; then
+        if [ -n "$new_session_id" ] && [ "$new_session_id" != "$base_session_id" ] && [ "$new_session_id" != "$pm_agent_session_id" ]; then
             break
         fi
         
@@ -1295,21 +1603,6 @@ cmd_start() {
     done
 
     if [ -z "$new_session_id" ]; then
-        if [ -f "$opencode_db" ]; then
-            local db_sessions=$(python3 -c "
-import sqlite3
-conn = sqlite3.connect('$opencode_db')
-cursor = conn.cursor()
-cursor.execute(\"SELECT id FROM session WHERE parent_id IS NOT NULL ORDER BY time_created DESC LIMIT 5\")
-for row in cursor.fetchall():
-    print(row[0])
-" 2>/dev/null || echo "")
-            if [ -n "$db_sessions" ]; then
-                echo "Recent forked sessions in DB:" >&2
-                echo "$db_sessions" >&2
-            fi
-        fi
-        
         echo "Error: Could not find newly created session after ${max_attempts}s" >&2
         if [ -n "$fork_log_output" ]; then
             echo "Fork log output:" >&2
@@ -1319,6 +1612,17 @@ for row in cursor.fetchall():
         exit 1
     fi
 
+    echo "Updating permissions for new session: $new_session_id"
+    python3 -c "
+import sqlite3
+conn = sqlite3.connect('$opencode_db')
+cursor = conn.cursor()
+PERMISSION_JSON = '[{\"permission\":\"question\",\"pattern\":\"*\",\"action\":\"deny\"},{\"permission\":\"plan_enter\",\"pattern\":\"*\",\"action\":\"deny\"},{\"permission\":\"plan_exit\",\"pattern\":\"*\",\"action\":\"deny\"},{\"permission\":\"external_directory\",\"pattern\":\"*\",\"action\":\"allow\"}]'
+cursor.execute('UPDATE session SET permission = ? WHERE id = ?', (PERMISSION_JSON, '$new_session_id'))
+conn.commit()
+print('[OK] Session permissions updated')
+"
+
     if [ "$DEBUG_MODE" = true ]; then
         echo "[DEBUG] Forked session permissions check:"
         python3 -c "
@@ -1333,8 +1637,25 @@ for row in cursor.fetchall():
 " 2>/dev/null || echo "  (failed to query DB)"
     fi
 
-    printf '{"type": "forked", "issue_ref": "%s", "opencode_session_id": "%s", "worktree_path": "%s", "created_at": "%s", "state": "idle"}\n' \
-        "$issue_ref" "$new_session_id" "$worktree_path" "$(date -Iseconds)" > "$SESSIONS_DIR/$session_file"
+    local branch_name=$(issue_ref_to_branch_name "$issue_ref")
+    
+    python3 << PYEOF > "$SESSIONS_DIR/$session_file"
+import json
+
+session = {
+    "type": "forked",
+    "issue_ref": "$issue_ref",
+    "opencode_session_id": "$new_session_id",
+    "worktree_path": "$worktree_path",
+    "created_at": "$(date -Iseconds)",
+    "state": "idle",
+    "branch_name": "$branch_name",
+    "pr_url": "$pr_url" if "$pr_url" else None
+}
+
+with open("$SESSIONS_DIR/$session_file", "w") as f:
+    json.dump(session, f, indent=2)
+PYEOF
 
     add_issue_to_index "$issue_ref" "$session_file"
 
@@ -1386,12 +1707,13 @@ cmd_continue() {
 
     echo "Continuing session for '$session_name'..."
     # Note: --continue always allowed (existing sessions don't count toward limit)
+    # Wrap in subshell with cd to ensure worktree directory is set correctly in session DB
     if [ -n "$worktree_path" ] && [ -d "$worktree_path" ]; then
         echo "Using worktree: $worktree_path"
         if [ "$DEBUG_MODE" = true ]; then
-            (cd "$worktree_path" && opencode run "$message" --continue --session "$opencode_session_id" 2>&1) | tee "$session_path.debug.log" &
+            (cd "$worktree_path" && opencode run "$message" --continue --session "$opencode_session_id" --dir "$worktree_path" 2>&1) | tee "$session_path.debug.log" &
         else
-            (cd "$worktree_path" && opencode run "$message" --continue --session "$opencode_session_id" 2>&1) &
+            (cd "$worktree_path" && opencode run "$message" --continue --session "$opencode_session_id" --dir "$worktree_path" 2>&1) &
         fi
     else
         if [ "$DEBUG_MODE" = true ]; then
@@ -1548,15 +1870,22 @@ cmd_destroy() {
 
     if [ "$target" = "base" ]; then
         if [ "$force" = true ]; then
+            local base_session_id=$(get_base_session_id)
+            local pm_agent_session_id=$(get_pm_agent_session_id)
             rm -f "$SESSIONS_DIR/base.json"
-            local pm_agent=$(get_pm_agent_session_id)
-            if [ -n "$pm_agent" ] && [ "$pm_agent" != "null" ]; then
-                rm -f "$SESSIONS_DIR/pm-agent.json"
-                echo '{"base": null, "pm_agent": null, "issues": {}}' > "$INDEX_FILE"
-            else
-                echo '{"base": null, "pm_agent": null, "issues": {}}' > "$INDEX_FILE"
+            rm -f "$SESSIONS_DIR/pm-agent.json"
+            rm -f "$SESSIONS_DIR/issue-"*.json 2>/dev/null || true
+            echo '{"base": null, "pm_agent": null, "issues": {}}' > "$INDEX_FILE"
+            
+            if [ -n "$base_session_id" ] && [ "$base_session_id" != "null" ]; then
+                echo "Deleting base session: $base_session_id"
+                opencode session delete "$base_session_id" 2>/dev/null || echo "Warning: Could not delete base session"
             fi
-            echo "Base session destroyed"
+            if [ -n "$pm_agent_session_id" ] && [ "$pm_agent_session_id" != "null" ]; then
+                echo "Deleting PM agent session: $pm_agent_session_id"
+                opencode session delete "$pm_agent_session_id" 2>/dev/null || echo "Warning: Could not delete PM agent session"
+            fi
+            echo "Base and PM agent sessions destroyed"
         else
             echo "Error: destroying base session requires --base -y" >&2
             exit 1
@@ -1566,6 +1895,7 @@ cmd_destroy() {
 
     if [ "$target" = "pm-agent" ]; then
         if [ "$force" = true ]; then
+            local pm_session_id=$(get_pm_agent_session_id)
             rm -f "$SESSIONS_DIR/pm-agent.json"
             local base=$(get_base_session_id)
             if [ -n "$base" ] && [ "$base" != "null" ]; then
@@ -1573,6 +1903,10 @@ cmd_destroy() {
             else
                 write_index "null" "null" "{}"
             fi
+            if [ -n "$pm_session_id" ] && [ "$pm_session_id" != "null" ]; then
+                echo "Deleting opencode session: $pm_session_id"
+                opencode session delete "$pm_session_id" 2>/dev/null || echo "Warning: Could not delete session from opencode (may already be deleted)"
+            fi
             echo "PM agent session destroyed"
         else
             echo "Error: destroying pm-agent session requires --pm-agent -y" >&2
@@ -1597,6 +1931,25 @@ cmd_destroy() {
         remove_issue_from_index "$target"
         echo "Session for '$target' destroyed"
     else
+        if [ "$WORKTREE_CHECK_PR_STATUS" = "true" ]; then
+            local pr_url=$(python3 -c "import json; print(json.load(open('$session_path')).get('pr_url', '') or '')" 2>/dev/null || echo "")
+            if [ -n "$pr_url" ] && [ "$pr_url" != "None" ]; then
+                echo "Checking PR status at '$pr_url'..."
+                local pr_status=$(check_pr_status "$pr_url")
+                if [ "$pr_status" = "open" ]; then
+                    echo "Error: PR is still open at $pr_url" >&2
+                    echo "Use --force to destroy anyway, or close the PR first" >&2
+                    exit 1
+                elif [ "$pr_status" = "merged" ]; then
+                    echo "PR has been merged. Safe to destroy."
+                elif [ "$pr_status" = "closed" ]; then
+                    echo "PR has been closed. Safe to destroy."
+                else
+                    echo "Warning: Could not determine PR status (got: $pr_status). Proceeding anyway." >&2
+                fi
+            fi
+        fi
+        
         echo "Delete session and worktree for '$target'? [y/N] "
         local reply
         read reply
@@ -1664,6 +2017,17 @@ main() {
         destroy)
             cmd_destroy "$@"
             ;;
+        set-pr)
+            local issue_ref="${1:-}"
+            local pr_url="${2:-}"
+            if [ -z "$issue_ref" ] || [ -z "$pr_url" ]; then
+                echo "Usage: kugetsu set-pr <issue-ref> <pr-url>" >&2
+                echo "Example: kugetsu set-pr github.com/shoko/kugetsu#14 https://github.com/shoko/kugetsu/pulls/123" >&2
+                exit 1
+            fi
+            validate_issue_ref "$issue_ref"
+            update_session_pr_url "$issue_ref" "$pr_url"
+            ;;
         *)
             echo "Error: unknown command '$command'" >&2
             usage