Merge pull request 'fix(kugetsu): destroy --base and --pm-agent actually delete opencode sessions' (#113) from fix/destroy-removes-opencode-session into main

Previously destroy only removed local session files but didn't delete
the sessions from opencode's database. This caused init to reuse the
same session with old context.

Now destroy calls 'opencode session delete <id>' to properly remove
the session from opencode.

skills/kugetsu/scripts/kugetsu

@@ -876,7 +876,7 @@ 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"
@@ -1107,6 +1107,22 @@ EOF
         exit 1
     fi
 
+    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: Current directory is not empty: $PWD" >&2
+        echo "This may cause project context to contaminate the base session." >&2
+        echo "Consider running kugetsu init from an empty directory." >&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 +1242,6 @@ 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
@@ -1242,14 +1252,18 @@ 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}"
     
+    > "$fork_log"
+     
+    fix_session_permissions
+    
     if [ "$DEBUG_MODE" = true ]; then
-        (cd "$worktree_path" && opencode run "$message" --fork --session "$base_session_id" 2>&1) | tee "$fork_log" &
+        (cd "$worktree_path" && opencode run "$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 "$message" --fork --session "$base_session_id" --dir "$worktree_path" 2>&1) >> "$fork_log" &
     fi
 
     local fork_pid=$!
@@ -1262,25 +1276,17 @@ 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
         
@@ -1293,21 +1299,6 @@ 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
@@ -1317,6 +1308,31 @@ 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 "
+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"
 
@@ -1373,9 +1389,9 @@ 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
@@ -1532,6 +1548,7 @@ cmd_destroy() {
 
     if [ "$target" = "base" ]; then
         if [ "$force" = true ]; then
+            local base_session_id=$(get_base_session_id)
             rm -f "$SESSIONS_DIR/base.json"
             local pm_agent=$(get_pm_agent_session_id)
             if [ -n "$pm_agent" ] && [ "$pm_agent" != "null" ]; then
@@ -1540,6 +1557,10 @@ cmd_destroy() {
             else
                 echo '{"base": null, "pm_agent": null, "issues": {}}' > "$INDEX_FILE"
             fi
+            if [ -n "$base_session_id" ] && [ "$base_session_id" != "null" ]; then
+                echo "Deleting opencode session: $base_session_id"
+                opencode session delete "$base_session_id" 2>/dev/null || echo "Warning: Could not delete session from opencode (may already be deleted)"
+            fi
             echo "Base session destroyed"
         else
             echo "Error: destroying base session requires --base -y" >&2
@@ -1550,6 +1571,7 @@ 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" ] && [ "$base" != "null" ]; then
@@ -1557,6 +1579,10 @@ cmd_destroy() {
             else
                 write_index "null" "null" "{}"
             fi
+            if [ -n "$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