fix(kugetsu): destroy --base now also deletes PM agent session

When destroying base session, we now also delete the PM agent session
and all issue session files. This ensures clean slate on re-init.

skills/kugetsu/scripts/kugetsu

@@ -394,6 +394,41 @@ 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"
@@ -876,7 +911,7 @@ 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 +1123,11 @@ 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 +1147,29 @@ 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
@@ -1226,12 +1289,6 @@ 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 +1299,24 @@ 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 +1329,17 @@ cmd_start() {
     while [ $attempt -le $max_attempts ]; do
         sleep 1
         
-        while IFS= read -r sess; do
+        new_session_id=$(python3 -c "
-            [ "$sess" = "$base_session_id" ] && continue
+import sqlite3
-            [ "$sess" = "$pm_agent_session_id" ] && continue
+conn = sqlite3.connect('$opencode_db')
-            
+cursor = conn.cursor()
-            local existed_before=false
+cursor.execute(\"SELECT id FROM session WHERE directory = '$worktree_path' ORDER BY time_created DESC LIMIT 1\")
-            for before_sess in "${before_sessions[@]}"; do
+result = cursor.fetchone()
-                if [ "$sess" = "$before_sess" ]; then
+if result:
-                    existed_before=true
+    print(result[0])
-                    break
+" 2>/dev/null || echo "")
-                fi
-            done
-            
-            if [ "$existed_before" = false ]; then
-                new_session_id="$sess"
-                break
-            fi
-        done < <(opencode session list 2>/dev/null | grep -oP '^ses_\w+')
         
-        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 +1352,6 @@ 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 +1361,17 @@ 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 "
@@ -1389,9 +1442,9 @@ cmd_continue() {
     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" &
+            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 "$opencode_session_id" 2>&1) &
+            opencode run "$message" --continue --session "$opencode_session_id" --dir "$worktree_path" 2>&1 &
         fi
     else
         if [ "$DEBUG_MODE" = true ]; then
@@ -1548,15 +1601,22 @@ 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)
+            rm -f "$SESSIONS_DIR/pm-agent.json"
-            if [ -n "$pm_agent" ] && [ "$pm_agent" != "null" ]; then
+            rm -f "$SESSIONS_DIR/issue-"*.json 2>/dev/null || true
-                rm -f "$SESSIONS_DIR/pm-agent.json"
+            echo '{"base": null, "pm_agent": null, "issues": {}}' > "$INDEX_FILE"
-                echo '{"base": null, "pm_agent": null, "issues": {}}' > "$INDEX_FILE"
+            
-            else
+            if [ -n "$base_session_id" ] && [ "$base_session_id" != "null" ]; then
-                echo '{"base": null, "pm_agent": null, "issues": {}}' > "$INDEX_FILE"
+                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 +1626,7 @@ 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" ] && [ "$base" != "null" ]; then
@@ -1573,6 +1634,10 @@ cmd_destroy() {
             else
                 write_index "null" "null" "{}"
             fi
+            if [ -n "$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