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

@@ -146,8 +146,9 @@ issue_ref_to_worktree_name() {
 
 issue_ref_to_worktree_path() {
     local issue_ref="$1"
+    local parent_dir="${2:-$WORKTREES_DIR}"
     local worktree_name=$(issue_ref_to_worktree_name "$issue_ref")
-    echo "$WORKTREES_DIR/$worktree_name"
+    echo "$parent_dir/.kugetsu-worktrees/$worktree_name"
 }
 
 issue_ref_to_branch_name() {
@@ -195,13 +196,15 @@ get_repo_url() {
 
 worktree_exists() {
     local issue_ref="$1"
-    local worktree_path=$(issue_ref_to_worktree_path "$issue_ref")
+    local parent_dir="${2:-$PWD}"
+    local worktree_path=$(issue_ref_to_worktree_path "$issue_ref" "$parent_dir")
     [ -d "$worktree_path" ]
 }
 
 create_worktree() {
     local issue_ref="$1"
-    local worktree_path=$(issue_ref_to_worktree_path "$issue_ref")
+    local parent_dir="${2:-$PWD}"
+    local worktree_path=$(issue_ref_to_worktree_path "$issue_ref" "$parent_dir")
     local branch_name=$(issue_ref_to_branch_name "$issue_ref")
     local repo_url=$(get_repo_url "$issue_ref")
     
@@ -211,9 +214,10 @@ create_worktree() {
         exit 1
     fi
     
-    ensure_worktree_dir
+    local worktree_parent_dir=$(dirname "$worktree_path")
+    mkdir -p "$worktree_parent_dir"
     
-    if worktree_exists "$issue_ref"; then
+    if worktree_exists "$issue_ref" "$parent_dir"; then
         echo "Removing existing worktree at '$worktree_path'..."
         git worktree remove "$worktree_path" 2>/dev/null || rm -rf "$worktree_path"
     fi
@@ -234,9 +238,10 @@ create_worktree() {
 
 remove_worktree_for_issue() {
     local issue_ref="$1"
-    local worktree_path=$(issue_ref_to_worktree_path "$issue_ref")
+    local parent_dir="${2:-$PWD}"
+    local worktree_path=$(issue_ref_to_worktree_path "$issue_ref" "$parent_dir")
     
-    if worktree_exists "$issue_ref"; then
+    if worktree_exists "$issue_ref" "$parent_dir"; then
         echo "Removing worktree at '$worktree_path'..."
         git worktree remove "$worktree_path" 2>/dev/null || rm -rf "$worktree_path"
     fi
@@ -389,6 +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"
@@ -871,7 +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"
@@ -1083,6 +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)
     
@@ -1102,6 +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
@@ -1215,17 +1283,12 @@ cmd_start() {
         exit 1
     fi
 
-    local worktree_path=$(issue_ref_to_worktree_path "$issue_ref")
-    create_worktree "$issue_ref"
+    local parent_dir="$PWD"
+    local worktree_path=$(issue_ref_to_worktree_path "$issue_ref" "$parent_dir")
+    create_worktree "$issue_ref" "$parent_dir"
 
     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
@@ -1233,48 +1296,96 @@ cmd_start() {
     if [ "$active_count" -ge "$MAX_CONCURRENT_AGENTS" ]; then
         echo "Error: Max concurrent agents ($MAX_CONCURRENT_AGENTS) reached" >&2
         echo "Active sessions: $active_count" >&2
-        remove_worktree_for_issue "$issue_ref"
+        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 [ "$DEBUG_MODE" = true ]; then
-        opencode run "$message" --fork --session "$base_session_id" --dir "$worktree_path" 2>&1 | tee "$SESSIONS_DIR/$session_file.debug.log" &
+        (cd "$worktree_path" && opencode run "$full_message" --fork --session "$base_session_id" --dir "$worktree_path" 2>&1) | tee "$fork_log" &
     else
-        opencode run "$message" --fork --session "$base_session_id" --dir "$worktree_path" 2>&1 &
+        (cd "$worktree_path" && opencode run "$full_message" --fork --session "$base_session_id" --dir "$worktree_path" 2>&1) >> "$fork_log" &
     fi
 
-    # Wait briefly for session to be created
-    sleep 1
-
-    # Find the new session by comparing before/after lists
-    # Skip any session that existed before the fork and skip base/pm-agent
+    local fork_pid=$!
+    
+    local max_attempts=10
+    local attempt=1
     local new_session_id=""
-    while IFS= read -r sess; do
-        # Skip base and pm-agent
-        [ "$sess" = "$base_session_id" ] && continue
-        [ "$sess" = "$pm_agent_session_id" ] && continue
+    local fork_log_output=""
+    
+    while [ $attempt -le $max_attempts ]; do
+        sleep 1
         
-        # Check if this session existed before
-        local existed_before=false
-        for before_sess in "${before_sessions[@]}"; do
-            if [ "$sess" = "$before_sess" ]; then
-                existed_before=true
-                break
-            fi
-        done
+        new_session_id=$(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 [ "$existed_before" = false ]; then
-            new_session_id="$sess"
+        if [ -n "$new_session_id" ] && [ "$new_session_id" != "$base_session_id" ] && [ "$new_session_id" != "$pm_agent_session_id" ]; then
             break
         fi
-    done < <(opencode session list 2>/dev/null | grep -oP '^ses_\w+')
+        
+        if ! kill -0 $fork_pid 2>/dev/null; then
+            fork_log_output=$(tail -20 "$fork_log" 2>/dev/null || echo "(log empty or unavailable)")
+            break
+        fi
+        
+        attempt=$((attempt + 1))
+    done
 
     if [ -z "$new_session_id" ]; then
-        echo "Error: Could not find newly created session" >&2
+        echo "Error: Could not find newly created session after ${max_attempts}s" >&2
+        if [ -n "$fork_log_output" ]; then
+            echo "Fork log output:" >&2
+            echo "$fork_log_output" >&2
+        fi
         remove_worktree_for_issue "$issue_ref"
         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 "
+import sqlite3
+conn = sqlite3.connect('$opencode_db')
+cursor = conn.cursor()
+cursor.execute(\"SELECT id, directory, permission FROM session WHERE id = '$new_session_id'\")
+for row in cursor.fetchall():
+    print('  ID:', row[0])
+    print('  Directory:', row[1])
+    print('  Permission:', row[2])
+" 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"
 
@@ -1490,15 +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)
-            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
@@ -1508,6 +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" ] && [ "$base" != "null" ]; then
@@ -1515,6 +1634,10 @@ cmd_destroy() {
             else
                 write_index "null" "null" "{}"
             fi
+            if [ -n "$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