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"
@@ -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: $(git rev-parse --show-toplevel 2>/dev/null || echo 'unknown')" >&2
+        fi
+        echo "" >&2
+        echo "Press Ctrl+C to cancel or wait 5 seconds to continue anyway..." >&2
+        sleep 5
+    fi
+
     echo "Starting TUI to create base session..."
     echo "Press Ctrl+C to cancel or wait for session to be created"
     sleep 2
@@ -1240,12 +1303,20 @@ cmd_start() {
     local fork_log="$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=$!
@@ -1371,9 +1442,9 @@ cmd_continue() {
     if [ -n "$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
@@ -1530,15 +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 "$SESSIONS_DIR/pm-agent.json"
+            rm -f "$SESSIONS_DIR/issue-"*.json 2>/dev/null || true
             echo '{"base": null, "pm_agent": null, "issues": {}}' > "$INDEX_FILE"
-            else
+            
-                echo '{"base": null, "pm_agent": null, "issues": {}}' > "$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
@@ -1548,6 +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" ] && [ "$base" != "null" ]; then
@@ -1555,6 +1634,10 @@ cmd_destroy() {
             else
                 write_index "null" "null" "{}"
             fi
+            if [ -n "$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