loki-mode 6.1.0 → 6.2.1

package/README.md

@@ -9,7 +9,7 @@
 [![Agent Types](https://img.shields.io/badge/Agent%20Types-41-blue)]()
 [![Autonomi](https://img.shields.io/badge/Autonomi-autonomi.dev-5B4EEA)](https://www.autonomi.dev/)
 
-**Current Version: v5.52.4**
+**Current Version: v6.2.1**
 
 ---
 

package/SKILL.md

@@ -3,7 +3,7 @@ name: loki-mode
 description: Multi-agent autonomous startup system. Triggers on "Loki Mode". Takes PRD to deployed product with minimal human intervention. Requires --dangerously-skip-permissions flag.
 ---
 
-# Loki Mode v6.1.0
+# Loki Mode v6.2.1
 
 **You are an autonomous agent. You make decisions. You do not ask questions. You do not stop.**
 
@@ -263,4 +263,4 @@ The following features are documented in skill modules but not yet fully automat
 | Quality gates 3-reviewer system | Implemented (v5.35.0) | 5 specialist reviewers in `skills/quality-gates.md`; execution in run.sh |
 | Benchmarks (HumanEval, SWE-bench) | Infrastructure only | Runner scripts and datasets exist in `benchmarks/`; no published results |
 
-**v6.1.0 | [Autonomi](https://www.autonomi.dev/) flagship product | ~260 lines core**
+**v6.2.1 | [Autonomi](https://www.autonomi.dev/) flagship product | ~260 lines core**

package/VERSION

@@ -1 +1 @@
-6.1.0
+6.2.1

package/autonomy/bmad-adapter.py

@@ -80,7 +80,7 @@ def parse_frontmatter(text: str) -> Tuple[Dict[str, Any], str]:
     """Extract YAML frontmatter from a markdown document.
 
     Returns (metadata_dict, body_without_frontmatter).
-    Handles simple YAML: scalars, lists (flow and block), quoted strings.
+    Handles simple YAML: scalars, lists (flow-style only; block-style not supported), quoted strings.
     Does NOT require PyYAML -- uses regex-based extraction.
     """
     stripped = text.lstrip()
@@ -514,9 +514,10 @@ def validate_chain(
             "message": "PRD frontmatter has no inputDocuments -- cannot verify product-brief linkage.",
         })
     else:
+        docs = input_docs if isinstance(input_docs, list) else [input_docs] if input_docs else []
         findings.append({
             "level": "info",
-            "message": f"PRD references input documents: {', '.join(input_docs)}",
+            "message": f"PRD references input documents: {', '.join(docs)}",
         })
 
     # 2. Missing artifacts

package/autonomy/loki

@@ -448,6 +448,12 @@ show_help() {
     echo "  --parallel         Enable parallel mode with git worktrees"
     echo "  --budget USD       Set cost budget limit"
     echo ""
+    echo "Progressive Isolation (for 'run'):"
+    echo "  --worktree, -w     Git worktree isolation (separate branch)"
+    echo "  --pr               Auto-create PR after completion (implies --worktree)"
+    echo "  --ship             Auto-merge after PR (implies --pr)"
+    echo "  --detach, -d       Run in background (implies --worktree)"
+    echo ""
     echo "Examples:"
     echo "  loki run 123                  # GitHub issue from current repo"
     echo "  loki run PROJ-456             # Jira issue"
@@ -640,8 +646,9 @@ cmd_start() {
     if [[ -n "$bmad_project_path" ]]; then
         # Resolve to absolute path
         if [[ ! "$bmad_project_path" = /* ]]; then
+            local original_bmad_path="$bmad_project_path"
             bmad_project_path="$(cd "$bmad_project_path" 2>/dev/null && pwd)" || {
-                echo -e "${RED}Error: BMAD project path does not exist: $bmad_project_path${NC}"
+                echo -e "${RED}Error: BMAD project path does not exist: $original_bmad_path${NC}"
                 exit 1
             }
         fi
@@ -2519,6 +2526,10 @@ cmd_run() {
     local start_args=()
     local no_start=false
     local provider_override=""
+    local use_worktree=false
+    local create_pr=false
+    local auto_merge=false
+    local run_detached=false
 
     # Parse arguments
     while [[ $# -gt 0 ]]; do
@@ -2551,6 +2562,14 @@ cmd_run() {
                 echo "  --sandbox          Run in Docker sandbox"
                 echo "  --budget USD       Set cost budget limit"
                 echo ""
+                echo "Progressive Isolation:"
+                echo "  --worktree, -w     Git worktree isolation (separate branch)"
+                echo "  --pr               Worktree + auto-create PR (implies --worktree)"
+                echo "  --ship             Worktree + PR + auto-merge (implies --pr)"
+                echo "  --detach, -d       Run in background (implies --worktree)"
+                echo ""
+                echo "  Cascade: --ship implies --pr implies --worktree"
+                echo ""
                 echo "Environment Variables:"
                 echo "  JIRA_API_TOKEN     Jira API token (for Jira issues)"
                 echo "  JIRA_URL           Jira base URL (for Jira issues)"
@@ -2563,6 +2582,10 @@ cmd_run() {
                 echo "  loki run https://gitlab.com/o/r/-/issues/42  # GitLab issue"
                 echo "  loki run 123 --dry-run                   # Preview PRD"
                 echo "  loki run 123 --parallel --provider codex # Parallel mode with Codex"
+                echo "  loki run 123 --worktree                  # Isolated branch"
+                echo "  loki run 123 --pr                        # Auto-create PR"
+                echo "  loki run 123 --ship                      # Full automation: PR + merge"
+                echo "  loki run 123 --ship -d                   # Background, full automation"
                 exit 0
                 ;;
             --dry-run)
@@ -2626,6 +2649,30 @@ cmd_run() {
                 start_args+=("--budget" "${1#*=}")
                 shift
                 ;;
+            --worktree|-w)
+                start_args+=("--parallel")
+                use_worktree=true
+                shift
+                ;;
+            --pr)
+                use_worktree=true
+                create_pr=true
+                start_args+=("--parallel")
+                shift
+                ;;
+            --ship)
+                use_worktree=true
+                create_pr=true
+                auto_merge=true
+                start_args+=("--parallel")
+                shift
+                ;;
+            --detach|-d)
+                use_worktree=true
+                run_detached=true
+                start_args+=("--parallel")
+                shift
+                ;;
             -*)
                 echo -e "${RED}Unknown option: $1${NC}"
                 echo "Run 'loki run --help' for usage."
@@ -2687,10 +2734,66 @@ cmd_run() {
     fi
     echo ""
 
+    # Progressive isolation: set up worktree branch naming
+    if $use_worktree; then
+        local branch_name="issue/${issue_provider}-${number:-$(date +%s)}"
+        log_info "Progressive isolation: branch $branch_name"
+        export LOKI_PARALLEL_MODE=true
+        export LOKI_WORKTREE_BRANCH="$branch_name"
+    fi
+
     # Generate PRD
     local prd_content
     prd_content=$(echo "$issue_json" | generate_prd_from_issue)
 
+    # Detached mode: fork to background
+    if $run_detached; then
+        local log_file="$LOKI_DIR/logs/run-${number:-$(date +%s)}.log"
+        mkdir -p "$(dirname "$log_file")"
+        echo -e "${GREEN}Running detached. Logs: $log_file${NC}"
+        echo -e "Check status: ${CYAN}loki status${NC}"
+
+        # Write PRD first so background process can use it
+        mkdir -p "$LOKI_DIR"
+        local detach_prd="$LOKI_DIR/prd-issue-${number}.md"
+        echo "$prd_content" > "$detach_prd"
+
+        if [[ -z "${branch_name:-}" ]]; then
+            branch_name="issue/detach-$(date +%s)"
+        fi
+
+        nohup bash -c "
+            cd $(pwd)
+            export LOKI_DETACHED=true
+            export LOKI_PARALLEL_MODE=true
+            export LOKI_WORKTREE_BRANCH=\"$branch_name\"
+            $(command -v loki || echo "$0") start \"$detach_prd\" --parallel ${start_args[*]+"${start_args[*]}"}
+
+            # Post-completion: create PR if requested
+            if [[ \"$create_pr\" == \"true\" ]]; then
+                branch_current=\$(git rev-parse --abbrev-ref HEAD 2>/dev/null || echo \"\")
+                if [[ -n \"\$branch_current\" && \"\$branch_current\" != \"main\" && \"\$branch_current\" != \"master\" ]]; then
+                    git push origin \"\$branch_current\" 2>/dev/null || true
+                    gh pr create --title \"${title:-Implementation for issue ${issue_ref}}\" --body \"Implemented by Loki Mode\" --head \"\$branch_current\" 2>/dev/null || true
+                fi
+            fi
+            # Post-completion: auto-merge if requested
+            if [[ \"$auto_merge\" == \"true\" ]]; then
+                branch_current=\$(git rev-parse --abbrev-ref HEAD 2>/dev/null || echo \"\")
+                if gh pr merge \"\$branch_current\" --squash --delete-branch 2>/dev/null; then
+                    if [[ -n \"${number:-}\" ]]; then
+                        gh issue close \"$number\" --comment \"Resolved by Loki Mode\" 2>/dev/null || true
+                    fi
+                fi
+            fi
+        " > "$log_file" 2>&1 &
+
+        local bg_pid=$!
+        echo "$bg_pid" > "$LOKI_DIR/run-${number:-detached}.pid"
+        echo "Background PID: $bg_pid"
+        return 0
+    fi
+
     # Handle dry-run
     if [[ "$dry_run" == "true" ]]; then
         echo -e "${BOLD}Generated PRD Preview:${NC}"
@@ -2728,6 +2831,77 @@ cmd_run() {
         echo ""
         echo -e "${GREEN}Starting Loki Mode with generated PRD...${NC}"
         cmd_start "$output_file" ${start_args[@]+"${start_args[@]}"}
+
+        # Progressive isolation: create PR
+        if $create_pr; then
+            echo ""
+            echo -e "${GREEN}Creating pull request...${NC}"
+            local pr_title="${title:-Implementation for issue ${issue_ref}}"
+            local pr_body="Implemented by Loki Mode (autonomous agent)
+
+Issue: ${issue_ref}
+Provider: ${issue_provider}
+
+## Changes
+$(git log --oneline "main..HEAD" 2>/dev/null || echo "See diff")"
+
+            case "${issue_provider:-github}" in
+                github)
+                    if command -v gh &>/dev/null; then
+                        local branch_current
+                        branch_current=$(git rev-parse --abbrev-ref HEAD 2>/dev/null || echo "")
+                        if [[ -n "$branch_current" && "$branch_current" != "main" && "$branch_current" != "master" ]]; then
+                            git push origin "$branch_current" 2>/dev/null || true
+                            gh pr create --title "$pr_title" --body "$pr_body" --head "$branch_current" 2>/dev/null && \
+                                echo -e "${GREEN}PR created${NC}" || \
+                                echo -e "${YELLOW}PR creation failed${NC}"
+                        fi
+                    fi
+                    ;;
+                gitlab)
+                    if command -v glab &>/dev/null; then
+                        local branch_current
+                        branch_current=$(git rev-parse --abbrev-ref HEAD 2>/dev/null || echo "")
+                        if [[ -n "$branch_current" && "$branch_current" != "main" && "$branch_current" != "master" ]]; then
+                            git push origin "$branch_current" 2>/dev/null || true
+                            glab mr create --title "$pr_title" --description "$pr_body" --source-branch "$branch_current" 2>/dev/null && \
+                                echo -e "${GREEN}MR created${NC}" || \
+                                echo -e "${YELLOW}MR creation failed${NC}"
+                        fi
+                    fi
+                    ;;
+                *)
+                    echo -e "${YELLOW}PR creation not supported for provider: $issue_provider${NC}"
+                    ;;
+            esac
+        fi
+
+        # Progressive isolation: auto-merge
+        if $auto_merge; then
+            echo -e "${GREEN}Auto-merging...${NC}"
+            case "${issue_provider:-github}" in
+                github)
+                    local branch_current
+                    branch_current=$(git rev-parse --abbrev-ref HEAD 2>/dev/null || echo "")
+                    if gh pr merge "$branch_current" --squash --delete-branch 2>/dev/null; then
+                        echo -e "${GREEN}PR merged and branch deleted${NC}"
+                        if [[ -n "${number:-}" ]]; then
+                            gh issue close "$number" --comment "Resolved by Loki Mode" 2>/dev/null || true
+                        fi
+                    else
+                        echo -e "${YELLOW}Auto-merge failed. PR remains open.${NC}"
+                    fi
+                    ;;
+                gitlab)
+                    glab mr merge --squash --remove-source-branch 2>/dev/null && \
+                        echo -e "${GREEN}MR merged and branch deleted${NC}" || \
+                        echo -e "${YELLOW}Auto-merge failed. MR remains open.${NC}"
+                    ;;
+                *)
+                    echo -e "${YELLOW}Auto-merge not supported for provider: $issue_provider${NC}"
+                    ;;
+            esac
+        fi
     fi
 }
 
@@ -6739,6 +6913,169 @@ cmd_migrate() {
     cmd_migrate_start "$codebase_path" "$target" "$plan_only" "$phase" "$parallel" "$compliance" "$dry_run" "$do_resume" "$multi_repo" "$export_report" "$no_dashboard" "$no_docs"
 }
 
+#===============================================================================
+# loki cluster - Custom workflow templates (v6.2.0)
+#===============================================================================
+
+cmd_cluster() {
+    local subcmd="${1:-list}"
+    shift 2>/dev/null || true
+
+    case "$subcmd" in
+        --help|-h|help)
+            echo -e "${BOLD}loki cluster${NC} - Custom workflow templates (v6.2.0)"
+            echo ""
+            echo "Usage: loki cluster <command> [options]"
+            echo ""
+            echo "Commands:"
+            echo "  list               List available workflow templates"
+            echo "  validate <name>    Validate a cluster template"
+            echo "  run <name> [args]  Execute a cluster workflow"
+            echo "  info <name>        Show template details"
+            echo ""
+            echo "Examples:"
+            echo "  loki cluster list"
+            echo "  loki cluster validate security-review"
+            echo "  loki cluster info code-review"
+            ;;
+        list)
+            echo -e "${BOLD}Available Cluster Templates${NC}"
+            echo ""
+            local template_dir="$SKILL_DIR/templates/clusters"
+            if [[ ! -d "$template_dir" ]]; then
+                echo "No templates found at $template_dir"
+                return 1
+            fi
+            for f in "$template_dir"/*.json; do
+                [[ ! -f "$f" ]] && continue
+                local name
+                name=$(basename "$f" .json)
+                local desc
+                desc=$(python3 -c "
+import json, sys
+try:
+    with open(sys.argv[1]) as f:
+        d = json.load(f)
+    print(d.get('description', 'No description'))
+except: print('Error reading template')
+" "$f" 2>/dev/null || echo "")
+                local agent_count
+                agent_count=$(python3 -c "
+import json, sys
+try:
+    with open(sys.argv[1]) as f:
+        d = json.load(f)
+    print(len(d.get('agents', [])))
+except: print('?')
+" "$f" 2>/dev/null || echo "?")
+                printf "  %-20s %s agents  %s\n" "$name" "$agent_count" "$desc"
+            done
+            ;;
+        validate)
+            local template_name="${1:-}"
+            if [[ -z "$template_name" ]]; then
+                echo -e "${RED}Usage: loki cluster validate <template-name>${NC}"
+                return 1
+            fi
+            local template_file="$SKILL_DIR/templates/clusters/${template_name}.json"
+            if [[ ! -f "$template_file" ]]; then
+                echo -e "${RED}Template not found: $template_name${NC}"
+                echo "Run 'loki cluster list' to see available templates."
+                return 1
+            fi
+            echo -e "${CYAN}Validating: $template_name${NC}"
+            local errors
+            errors=$(python3 -c "
+import json, sys
+sys.path.insert(0, '$SKILL_DIR')
+from swarm.patterns import TopologyValidator
+errors = TopologyValidator.validate_file(sys.argv[1])
+if errors:
+    for e in errors:
+        print(f'ERROR: {e}')
+else:
+    print('VALID')
+" "$template_file" 2>&1)
+            if echo "$errors" | grep -q "^VALID$"; then
+                echo -e "${GREEN}Template is valid${NC}"
+                return 0
+            else
+                echo -e "${RED}Validation errors:${NC}"
+                echo "$errors"
+                return 1
+            fi
+            ;;
+        info)
+            local template_name="${1:-}"
+            if [[ -z "$template_name" ]]; then
+                echo -e "${RED}Usage: loki cluster info <template-name>${NC}"
+                return 1
+            fi
+            local template_file="$SKILL_DIR/templates/clusters/${template_name}.json"
+            if [[ ! -f "$template_file" ]]; then
+                echo -e "${RED}Template not found: $template_name${NC}"
+                return 1
+            fi
+            python3 -c "
+import json, sys
+with open(sys.argv[1]) as f:
+    d = json.load(f)
+print(f\"Name:        {d.get('name', 'unknown')}\")
+print(f\"Description: {d.get('description', 'none')}\")
+print(f\"Version:     {d.get('version', 'unknown')}\")
+print(f\"Topology:    {d.get('topology', 'unknown')}\")
+print(f\"Agents:      {len(d.get('agents', []))}\")
+print()
+for a in d.get('agents', []):
+    subs = ', '.join(a.get('subscribes', []))
+    pubs = ', '.join(a.get('publishes', []))
+    print(f\"  [{a['id']}] ({a.get('type', '?')})\")
+    print(f\"    Role: {a.get('role', '?')}\")
+    print(f\"    Subscribes: {subs}\")
+    print(f\"    Publishes:  {pubs}\")
+    print()
+" "$template_file"
+            ;;
+        run)
+            local template_name="${1:-}"
+            if [[ -z "$template_name" ]]; then
+                echo -e "${RED}Usage: loki cluster run <template-name> [args]${NC}"
+                return 1
+            fi
+            local template_file="$SKILL_DIR/templates/clusters/${template_name}.json"
+            if [[ ! -f "$template_file" ]]; then
+                echo -e "${RED}Template not found: $template_name${NC}"
+                return 1
+            fi
+            # Validate first
+            local result
+            result=$(python3 -c "
+import json, sys
+sys.path.insert(0, '$SKILL_DIR')
+from swarm.patterns import TopologyValidator
+errors = TopologyValidator.validate_file(sys.argv[1])
+if errors:
+    for e in errors: print(f'ERROR: {e}')
+else:
+    print('VALID')
+" "$template_file" 2>&1)
+            if ! echo "$result" | grep -q "^VALID$"; then
+                echo -e "${RED}Template validation failed:${NC}"
+                echo "$result"
+                return 1
+            fi
+            echo -e "${GREEN}Cluster template: $template_name${NC}"
+            echo -e "${YELLOW}Note: Cluster execution engine is planned for v6.3.0.${NC}"
+            echo -e "Template validated successfully. Use 'loki cluster info $template_name' for details."
+            ;;
+        *)
+            echo -e "${RED}Unknown cluster command: $subcmd${NC}"
+            echo "Run 'loki cluster --help' for usage."
+            return 1
+            ;;
+    esac
+}
+
 # Main command dispatcher
 main() {
     if [ $# -eq 0 ]; then
@@ -6869,6 +7206,9 @@ main() {
         migrate)
             cmd_migrate "$@"
             ;;
+        cluster)
+            cmd_cluster "$@"
+            ;;
         metrics)
             cmd_metrics "$@"
             ;;

package/autonomy/prd-analyzer.py

@@ -114,7 +114,6 @@ DIMENSIONS = {
         "weight": 0.75,
         "heading_patterns": [
             r"(?i)#+\s.*(?:deploy|hosting|infra|ci.?cd|environment)",
-            r"(?i)^##\s+Non-Functional\s+Requirements",
         ],
         "content_patterns": [
             r"(?i)\b(?:deploy|hosting|ci.?cd|pipeline|staging|production)\b",
@@ -259,8 +258,9 @@ class PrdAnalyzer:
             if in_feature_section and re.match(r"^\s*#+\s", line):
                 in_feature_section = False
                 continue
-            if re.match(r"^\s*[-*]\s+\S", line) or re.match(r"^\s*\d+\.\s+\S", line):
-                count += 1
+            if in_feature_section:
+                if re.match(r"^\s*[-*]\s+\S", line) or re.match(r"^\s*\d+\.\s+\S", line):
+                    count += 1
 
         self.feature_count = count
         for threshold, label in SCOPE_THRESHOLDS:

package/autonomy/run.sh

@@ -7043,7 +7043,19 @@ except: pass
         fi
         local bmad_tasks=""
         if [[ -f ".loki/bmad-tasks.json" ]]; then
-            bmad_tasks=$(head -c 32000 ".loki/bmad-tasks.json")
+            bmad_tasks=$(python3 -c "
+import json, sys
+try:
+    with open('.loki/bmad-tasks.json') as f:
+        data = json.load(f)
+    out = json.dumps(data, indent=None)
+    if len(out) > 32000 and isinstance(data, list):
+        while len(json.dumps(data, indent=None)) > 32000 and data:
+            data.pop()
+        out = json.dumps(data, indent=None)
+    print(out[:32000])
+except: pass
+" 2>/dev/null)
         fi
         local bmad_validation=""
         if [[ -f ".loki/bmad-validation.md" ]]; then
@@ -7100,7 +7112,7 @@ populate_bmad_queue() {
     mkdir -p ".loki/queue"
 
     # Read BMAD tasks and create queue entries
-    python3 << 'BMAD_QUEUE_EOF' 2>/dev/null
+    python3 << 'BMAD_QUEUE_EOF'
 import json
 import os
 import sys
@@ -7155,12 +7167,16 @@ if os.path.exists(pending_path):
     except (json.JSONDecodeError, FileNotFoundError):
         existing = []
 
-# Convert BMAD stories to queue task format
+# Convert BMAD stories to queue task format (with deduplication)
+existing_ids = {t.get("id") for t in existing if isinstance(t, dict)}
 for i, story in enumerate(stories):
     if not isinstance(story, dict):
         continue
+    task_id = f"bmad-{i+1}"
+    if task_id in existing_ids:
+        continue
     task = {
-        "id": f"bmad-{i+1}",
+        "id": task_id,
         "title": story.get("title", story.get("name", f"BMAD Story {i+1}")),
         "description": story.get("description", story.get("action", "")),
         "priority": story.get("priority", "medium"),

package/autonomy/sandbox.sh

@@ -62,6 +62,35 @@ DASHBOARD_PORT="${LOKI_DASHBOARD_PORT:-57374}"
 # Security: Prompt injection disabled by default for enterprise security
 PROMPT_INJECTION_ENABLED="${LOKI_PROMPT_INJECTION:-false}"
 
+#===============================================================================
+# Docker Credential Mount Presets
+#===============================================================================
+
+# Preset definitions: "host_path:container_path:mode"
+# Container runs as user 'loki' (UID 1000), so mount to /home/loki/
+declare -A DOCKER_MOUNT_PRESETS
+DOCKER_MOUNT_PRESETS=(
+    # Note: gh and git are also hardcoded in start_sandbox() defaults
+    [gh]="$HOME/.config/gh:/home/loki/.config/gh:ro"
+    [git]="$HOME/.gitconfig:/home/loki/.gitconfig:ro"
+    [ssh]="$HOME/.ssh/known_hosts:/home/loki/.ssh/known_hosts:ro"
+    [aws]="$HOME/.aws:/home/loki/.aws:ro"
+    [azure]="$HOME/.azure:/home/loki/.azure:ro"
+    [kube]="$HOME/.kube:/home/loki/.kube:ro"
+    [terraform]="$HOME/.terraform.d:/home/loki/.terraform.d:ro"
+    [gcloud]="$HOME/.config/gcloud:/home/loki/.config/gcloud:ro"
+    [npm]="$HOME/.npmrc:/home/loki/.npmrc:ro"
+)
+
+# Environment variables auto-passed per preset (comma-separated)
+declare -A DOCKER_ENV_PRESETS
+DOCKER_ENV_PRESETS=(
+    [aws]="AWS_REGION,AWS_PROFILE,AWS_DEFAULT_REGION"
+    [azure]="AZURE_SUBSCRIPTION_ID,AZURE_TENANT_ID"
+    [gcloud]="GOOGLE_PROJECT,GOOGLE_REGION,GCLOUD_PROJECT"
+    [terraform]="TF_VAR_*"
+)
+
 #===============================================================================
 # Utility Functions
 #===============================================================================
@@ -767,9 +796,133 @@ docker_desktop_sandbox_run() {
 # Docker Container Sandbox (standard Docker - fallback from Docker Desktop)
 #===============================================================================
 
+# Resolve Docker credential mount presets
+# Reads from: .loki/config/settings.json dockerMounts, LOKI_DOCKER_MOUNTS env var
+# Returns: string of -v and -e flags for docker run
+resolve_docker_mounts() {
+    RESOLVED_MOUNTS=()
+
+    # Read configured presets (JSON array of strings)
+    local presets_json=""
+    if [[ -f "${PROJECT_DIR}/.loki/config/settings.json" ]]; then
+        presets_json=$(python3 -c "
+import json, sys
+try:
+    with open(sys.argv[1] + '/.loki/config/settings.json') as f:
+        print(json.dumps(json.load(f).get('dockerMounts', [])))
+except: print('[]')
+" "${PROJECT_DIR}" 2>/dev/null || echo "[]")
+    fi
+
+    # Override with env var if set
+    if [[ -n "${LOKI_DOCKER_MOUNTS:-}" ]]; then
+        presets_json="$LOKI_DOCKER_MOUNTS"
+    fi
+
+    # Parse and resolve
+    if [[ "$presets_json" != "[]" ]] && [[ "$presets_json" != "" ]]; then
+        local preset_names
+        preset_names=$(python3 -c "
+import json, sys
+try:
+    data = json.loads(sys.argv[1])
+    if isinstance(data, list):
+        for item in data:
+            print(item)
+except: pass
+" "$presets_json" 2>/dev/null || echo "")
+
+        local name
+        while IFS= read -r name; do
+            [[ -z "$name" ]] && continue
+
+            local preset_value="${DOCKER_MOUNT_PRESETS[$name]:-}"
+            if [[ -z "$preset_value" ]]; then
+                log_warn "Unknown Docker mount preset: $name"
+                continue
+            fi
+
+            IFS=':' read -ra parts <<< "$preset_value"
+            local host_path="${parts[0]}"
+            local container_path="${parts[1]}"
+            local mode="${parts[2]:-ro}"
+
+            # Safe tilde expansion (no eval)
+            if [[ "$host_path" == "~/"* ]]; then
+                host_path="$HOME/${host_path#\~/}"
+            elif [[ "$host_path" == "~" ]]; then
+                host_path="$HOME"
+            fi
+
+            # Only mount if host path exists
+            if [[ -e "$host_path" ]]; then
+                RESOLVED_MOUNTS+=("-v" "${host_path}:${container_path}:${mode}")
+                log_info "  Mount preset [$name]: $host_path -> $container_path ($mode)"
+            fi
+
+            # Add associated env vars
+            local env_list="${DOCKER_ENV_PRESETS[$name]:-}"
+            if [[ -n "$env_list" ]]; then
+                IFS=',' read -ra env_names <<< "$env_list"
+                local env_name
+                for env_name in "${env_names[@]}"; do
+                    if [[ "$env_name" == *"*" ]]; then
+                        # Wildcard: pass all matching env vars
+                        local prefix="${env_name%\*}"
+                        while IFS='=' read -r key val; do
+                            [[ "$key" == "$prefix"* ]] && [[ -n "$val" ]] && {
+                                RESOLVED_MOUNTS+=("-e" "$key")
+                                log_info "    Env wildcard [$name]: passing $key"
+                            }
+                        done < <(env)
+                    elif [[ -n "${!env_name:-}" ]]; then
+                        RESOLVED_MOUNTS+=("-e" "$env_name")
+                    fi
+                done
+            fi
+        done <<< "$preset_names"
+    fi
+}
+
 start_sandbox() {
-    local prd_path="${1:-}"
+    # Parse arguments: extract flags before positional args
+    local prd_path=""
     local provider="${LOKI_PROVIDER:-claude}"
+    local no_mounts=false
+    local -a custom_mounts=()
+
+    while [[ $# -gt 0 ]]; do
+        case "$1" in
+            --mount)
+                if [[ -n "${2:-}" ]]; then
+                    custom_mounts+=("$2")
+                    shift 2
+                else
+                    log_error "--mount requires HOST:CONTAINER:MODE argument"
+                    return 1
+                fi
+                ;;
+            --no-mounts)
+                no_mounts=true
+                shift
+                ;;
+            --provider)
+                if [[ -n "${2:-}" ]]; then
+                    provider="$2"
+                    shift 2
+                else
+                    shift
+                fi
+                ;;
+            *)
+                # First non-flag argument is the PRD path
+                if [[ -z "$prd_path" ]]; then
+                    prd_path="$1"
+                fi
+                shift
+                ;;
+        esac
+    done
 
     # Set up signal handler to cleanup on Ctrl+C
     trap cleanup_container INT TERM
@@ -887,6 +1040,41 @@ start_sandbox() {
         docker_args+=("--volume" "$HOME/.config/gh:/home/loki/.config/gh:ro")
     fi
 
+    # Apply Docker credential mount presets (additive on top of defaults above)
+    if [[ "$no_mounts" != "true" ]] && [[ "${LOKI_NO_DOCKER_MOUNTS:-}" != "true" ]]; then
+        resolve_docker_mounts
+        if [[ ${#RESOLVED_MOUNTS[@]} -gt 0 ]]; then
+            docker_args+=("${RESOLVED_MOUNTS[@]}")
+        fi
+    fi
+
+    # Apply custom --mount arguments
+    local custom_mount
+    for custom_mount in "${custom_mounts[@]+"${custom_mounts[@]}"}"; do
+        if [[ -n "$custom_mount" ]]; then
+            IFS=':' read -ra mount_parts <<< "$custom_mount"
+            local c_host="${mount_parts[0]:-}"
+            local c_container="${mount_parts[1]:-}"
+            local c_mode="${mount_parts[2]:-ro}"
+            if [[ -n "$c_host" ]] && [[ -n "$c_container" ]]; then
+                # Safe tilde expansion (no eval)
+                if [[ "$c_host" == "~/"* ]]; then
+                    c_host="$HOME/${c_host#\~/}"
+                elif [[ "$c_host" == "~" ]]; then
+                    c_host="$HOME"
+                fi
+                if [[ -e "$c_host" ]]; then
+                    docker_args+=("--volume" "${c_host}:${c_container}:${c_mode}")
+                    log_info "  Custom mount: $c_host -> $c_container ($c_mode)"
+                else
+                    log_warn "Custom mount source does not exist: $c_host"
+                fi
+            else
+                log_warn "Invalid mount format: $custom_mount (expected HOST:CONTAINER[:MODE])"
+            fi
+        fi
+    done
+
     # Pass API keys as environment variables (more secure than mounting files)
     if [[ -n "${ANTHROPIC_API_KEY:-}" ]]; then
         docker_args+=("--env" "ANTHROPIC_API_KEY")

package/dashboard/__init__.py

@@ -7,7 +7,7 @@ Modules:
     control: Session control API (start/stop/pause/resume)
 """
 
-__version__ = "6.1.0"
+__version__ = "6.2.1"
 
 # Expose the control app for easy import
 try:

package/docs/INSTALLATION.md

@@ -2,33 +2,28 @@
 
 The flagship product of [Autonomi](https://www.autonomi.dev/). Complete installation instructions for all platforms and use cases.
 
-**Version:** v6.1.0
+**Version:** v6.2.1
 
 ---
 
-## What's New in v5.49.1
-
-### Enterprise Security (v5.36.0-v5.37.1)
-- TLS/HTTPS support for dashboard connections
-- OIDC/SSO authentication (Google, Azure AD, Okta)
-- RBAC roles (admin, operator, viewer, auditor)
-- WebSocket authentication for real-time connections
-- Syslog forwarding for SIEM integration
-- Non-root Docker with SETUID/SETGID removed
-- Salted token hashing and rate limiting
-
-### Monitoring & Observability (v5.38.0)
-- Prometheus/OpenMetrics `/metrics` endpoint with 9 metrics
-- `loki metrics` CLI command
-- Agent action audit trail at `.loki/logs/agent-audit.jsonl`
-- `loki audit` CLI with log/count subcommands
-- SHA-256 chain-hashed tamper-evident audit entries
-
-### Workflow Protection (v5.38.0)
-- Branch protection: agent sessions auto-create feature branches
-- PR creation via `gh` on session completion
-- OpenClaw bridge foundation for external integrations
-- Network security documentation (Docker/Kubernetes)
+## What's New in v6.2.1
+
+### Dual-Mode Architecture (v6.0.0)
+- `loki run` command for direct autonomous execution
+- Dual-mode: skill mode (inside Claude Code) and standalone mode
+- Dynamic model resolution across all providers
+- Multi-provider issue fixes and stability improvements
+
+### ChromaDB Semantic Code Search (v6.1.0)
+- Semantic code search via ChromaDB vector database
+- MCP integration with `loki_code_search` and `loki_code_search_stats` tools
+- Automatic codebase indexing with `tools/index-codebase.py`
+
+### Memory System (v5.15.0+)
+- Episodic, semantic, and procedural memory layers
+- Progressive disclosure with 3-layer loading
+- Token economics tracking for discovery vs read tokens
+- Optional vector search with sentence-transformers
 
 ---
 

package/mcp/__init__.py

@@ -57,4 +57,4 @@ try:
 except ImportError:
     __all__ = ['mcp']
 
-__version__ = '6.1.0'
+__version__ = '6.2.1'

package/mcp/server.py

@@ -1231,10 +1231,15 @@ def _get_chroma_collection():
     """Get or create ChromaDB collection (lazy connection)."""
     global _chroma_client, _chroma_collection
     if _chroma_collection is not None:
-        return _chroma_collection
+        try:
+            _chroma_client.heartbeat()
+            return _chroma_collection
+        except Exception:
+            _chroma_client = None
+            _chroma_collection = None
     try:
         import chromadb
-        _chroma_client = chromadb.HttpClient(host=CHROMA_HOST, port=int(CHROMA_PORT))
+        _chroma_client = chromadb.HttpClient(host=CHROMA_HOST, port=CHROMA_PORT)
         _chroma_collection = _chroma_client.get_collection(name=CHROMA_COLLECTION)
         return _chroma_collection
     except Exception as e:

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "loki-mode",
-  "version": "6.1.0",
+  "version": "6.2.1",
   "description": "Loki Mode by Autonomi - Multi-agent autonomous startup system for Claude Code, Codex CLI, and Gemini CLI",
   "keywords": [
     "agent",

package/templates/clusters/README.md

@@ -0,0 +1,21 @@
+# Cluster Templates
+
+Pre-built workflow topologies for common development patterns.
+
+## Usage
+
+    loki cluster list                    # List available templates
+    loki cluster validate <template>     # Validate topology
+    loki cluster run <template> [args]   # Execute workflow
+
+## Template Format
+
+Each template is a JSON file defining agents, their pub/sub topics,
+and the workflow topology.
+
+## Available Templates
+
+- security-review: Multi-agent security audit pipeline
+- performance-audit: Performance analysis with profiling
+- refactoring: Structured refactoring with test preservation
+- code-review: Multi-reviewer code review process

package/templates/clusters/code-review.json

@@ -0,0 +1,36 @@
+{
+    "name": "Code Review",
+    "description": "Multi-reviewer code review with conflict resolution",
+    "version": "1.0.0",
+    "topology": "fan-out-fan-in",
+    "agents": [
+        {
+            "id": "reviewer-arch",
+            "type": "review-code",
+            "role": "Review architecture and design patterns",
+            "subscribes": ["task.start"],
+            "publishes": ["review.architecture"]
+        },
+        {
+            "id": "reviewer-security",
+            "type": "review-security",
+            "role": "Review security implications",
+            "subscribes": ["task.start"],
+            "publishes": ["review.security"]
+        },
+        {
+            "id": "reviewer-tests",
+            "type": "eng-qa",
+            "role": "Review test coverage and quality",
+            "subscribes": ["task.start"],
+            "publishes": ["review.tests"]
+        },
+        {
+            "id": "resolver",
+            "type": "review-code",
+            "role": "Synthesize all review findings and resolve conflicts",
+            "subscribes": ["review.architecture", "review.security", "review.tests"],
+            "publishes": ["task.complete"]
+        }
+    ]
+}

package/templates/clusters/performance-audit.json

@@ -0,0 +1,29 @@
+{
+    "name": "Performance Audit",
+    "description": "Performance analysis with profiling and optimization recommendations",
+    "version": "1.0.0",
+    "topology": "fan-out-fan-in",
+    "agents": [
+        {
+            "id": "profiler",
+            "type": "eng-perf",
+            "role": "Profile application and identify bottlenecks",
+            "subscribes": ["task.start"],
+            "publishes": ["profile.results"]
+        },
+        {
+            "id": "db-analyzer",
+            "type": "eng-database",
+            "role": "Analyze database queries and index usage",
+            "subscribes": ["task.start"],
+            "publishes": ["db.analysis"]
+        },
+        {
+            "id": "optimizer",
+            "type": "eng-perf",
+            "role": "Generate optimization recommendations from all analyses",
+            "subscribes": ["profile.results", "db.analysis"],
+            "publishes": ["task.complete"]
+        }
+    ]
+}

package/templates/clusters/refactoring.json

@@ -0,0 +1,29 @@
+{
+    "name": "Refactoring",
+    "description": "Structured refactoring with test preservation and review",
+    "version": "1.0.0",
+    "topology": "pipeline",
+    "agents": [
+        {
+            "id": "analyzer",
+            "type": "review-code",
+            "role": "Analyze code for refactoring opportunities",
+            "subscribes": ["task.start"],
+            "publishes": ["analysis.complete"]
+        },
+        {
+            "id": "refactorer",
+            "type": "eng-backend",
+            "role": "Apply refactoring changes with test preservation",
+            "subscribes": ["analysis.complete"],
+            "publishes": ["refactor.complete"]
+        },
+        {
+            "id": "verifier",
+            "type": "eng-qa",
+            "role": "Verify all tests pass and behavior is preserved",
+            "subscribes": ["refactor.complete"],
+            "publishes": ["task.complete"]
+        }
+    ]
+}

package/templates/clusters/security-review.json

@@ -0,0 +1,36 @@
+{
+    "name": "Security Review",
+    "description": "Multi-agent security audit with adversarial testing",
+    "version": "1.0.0",
+    "topology": "pipeline",
+    "agents": [
+        {
+            "id": "scanner",
+            "type": "ops-security",
+            "role": "Run SAST/dependency scanning on codebase",
+            "subscribes": ["task.start"],
+            "publishes": ["scan.results"]
+        },
+        {
+            "id": "reviewer",
+            "type": "review-security",
+            "role": "Review findings from scanner, assess severity",
+            "subscribes": ["scan.results"],
+            "publishes": ["review.findings"]
+        },
+        {
+            "id": "adversarial",
+            "type": "review-security",
+            "role": "Attempt to exploit discovered vulnerabilities",
+            "subscribes": ["review.findings"],
+            "publishes": ["exploit.results"]
+        },
+        {
+            "id": "reporter",
+            "type": "prod-techwriter",
+            "role": "Compile security report from all findings",
+            "subscribes": ["scan.results", "review.findings", "exploit.results"],
+            "publishes": ["task.complete"]
+        }
+    ]
+}