loki-mode 6.2.0 → 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 v6.2.0
+# 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 |
 
-**v6.2.0 | [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 @@
-6.2.0
+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

@@ -646,8 +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
@@ -2754,10 +2755,12 @@ cmd_run() {
 
         # Write PRD first so background process can use it
         mkdir -p "$LOKI_DIR"
-        local prd_content_detach
-        prd_content_detach=$(echo "$issue_json" | generate_prd_from_issue)
         local detach_prd="$LOKI_DIR/prd-issue-${number}.md"
-        echo "$prd_content_detach" > "$detach_prd"
+        echo "$prd_content" > "$detach_prd"
+
+        if [[ -z "${branch_name:-}" ]]; then
+            branch_name="issue/detach-$(date +%s)"
+        fi
 
         nohup bash -c "
             cd $(pwd)
@@ -2765,6 +2768,24 @@ cmd_run() {
             export LOKI_PARALLEL_MODE=true
             export LOKI_WORKTREE_BRANCH=\"$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=$!
@@ -2862,11 +2883,13 @@ $(git log --oneline "main..HEAD" 2>/dev/null || echo "See diff")"
                 github)
                     local branch_current
                     branch_current=$(git rev-parse --abbrev-ref HEAD 2>/dev/null || echo "")
-                    gh pr merge "$branch_current" --squash --delete-branch 2>/dev/null && \
-                        echo -e "${GREEN}PR merged and branch deleted${NC}" || \
+                    if gh pr merge "$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}"
-                    if [[ -n "${number:-}" ]]; then
-                        gh issue close "$number" --comment "Resolved by Loki Mode" 2>/dev/null || true
                     fi
                     ;;
                 gitlab)
@@ -6964,7 +6987,6 @@ except: print('?')
             local errors
             errors=$(python3 -c "
 import json, sys
-sys.path.insert(0, '$(dirname "$SKILL_DIR/swarm/")')
 sys.path.insert(0, '$SKILL_DIR')
 from swarm.patterns import TopologyValidator
 errors = TopologyValidator.validate_file(sys.argv[1])
@@ -7026,17 +7048,20 @@ for a in d.get('agents', []):
                 return 1
             fi
             # Validate first
-            local errors
-            errors=$(python3 -c "
+            local result
+            result=$(python3 -c "
 import json, sys
 sys.path.insert(0, '$SKILL_DIR')
 from swarm.patterns import TopologyValidator
 errors = TopologyValidator.validate_file(sys.argv[1])
-for e in errors: print(e)
+if errors:
+    for e in errors: print(f'ERROR: {e}')
+else:
+    print('VALID')
 " "$template_file" 2>&1)
-            if [[ -n "$errors" ]]; then
+            if ! echo "$result" | grep -q "^VALID$"; then
                 echo -e "${RED}Template validation failed:${NC}"
-                echo "$errors"
+                echo "$result"
                 return 1
             fi
             echo -e "${GREEN}Cluster template: $template_name${NC}"

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

@@ -70,9 +70,10 @@ PROMPT_INJECTION_ENABLED="${LOKI_PROMPT_INJECTION:-false}"
 # Container runs as user 'loki' (UID 1000), so mount to /home/loki/
 declare -A DOCKER_MOUNT_PRESETS
 DOCKER_MOUNT_PRESETS=(
+    # Note: gh and git are also hardcoded in start_sandbox() defaults
     [gh]="$HOME/.config/gh:/home/loki/.config/gh:ro"
     [git]="$HOME/.gitconfig:/home/loki/.gitconfig:ro"
-    [ssh]="$HOME/.ssh:/home/loki/.ssh: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"
@@ -799,7 +800,7 @@ docker_desktop_sandbox_run() {
 # 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() {
-    local mount_args=""
+    RESOLVED_MOUNTS=()
 
     # Read configured presets (JSON array of strings)
     local presets_json=""
@@ -807,10 +808,10 @@ resolve_docker_mounts() {
         presets_json=$(python3 -c "
 import json, sys
 try:
-    with open('${PROJECT_DIR}/.loki/config/settings.json') as f:
+    with open(sys.argv[1] + '/.loki/config/settings.json') as f:
         print(json.dumps(json.load(f).get('dockerMounts', [])))
 except: print('[]')
-" 2>/dev/null || echo "[]")
+" "${PROJECT_DIR}" 2>/dev/null || echo "[]")
     fi
 
     # Override with env var if set
@@ -846,12 +847,16 @@ except: pass
             local container_path="${parts[1]}"
             local mode="${parts[2]:-ro}"
 
-            # Expand ~ and $HOME
-            host_path=$(eval echo "$host_path" 2>/dev/null || echo "$host_path")
+            # 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 "$host_path" ]]; then
-                mount_args="$mount_args -v ${host_path}:${container_path}:${mode}"
+                RESOLVED_MOUNTS+=("-v" "${host_path}:${container_path}:${mode}")
                 log_info "  Mount preset [$name]: $host_path -> $container_path ($mode)"
             fi
 
@@ -865,18 +870,18 @@ except: pass
                         # Wildcard: pass all matching env vars
                         local prefix="${env_name%\*}"
                         while IFS='=' read -r key val; do
-                            [[ "$key" == "$prefix"* ]] && [[ -n "$val" ]] && \
-                                mount_args="$mount_args -e $key"
+                            [[ "$key" == "$prefix"* ]] && [[ -n "$val" ]] && {
+                                RESOLVED_MOUNTS+=("-e" "$key")
+                                log_info "    Env wildcard [$name]: passing $key"
+                            }
                         done < <(env)
                     elif [[ -n "${!env_name:-}" ]]; then
-                        mount_args="$mount_args -e $env_name"
+                        RESOLVED_MOUNTS+=("-e" "$env_name")
                     fi
                 done
             fi
         done <<< "$preset_names"
     fi
-
-    echo "$mount_args"
 }
 
 start_sandbox() {
@@ -1037,11 +1042,9 @@ start_sandbox() {
 
     # Apply Docker credential mount presets (additive on top of defaults above)
     if [[ "$no_mounts" != "true" ]] && [[ "${LOKI_NO_DOCKER_MOUNTS:-}" != "true" ]]; then
-        local preset_mounts
-        preset_mounts=$(resolve_docker_mounts)
-        if [[ -n "$preset_mounts" ]]; then
-            # shellcheck disable=SC2206
-            docker_args+=($preset_mounts)
+        resolve_docker_mounts
+        if [[ ${#RESOLVED_MOUNTS[@]} -gt 0 ]]; then
+            docker_args+=("${RESOLVED_MOUNTS[@]}")
         fi
     fi
 
@@ -1054,7 +1057,12 @@ start_sandbox() {
             local c_container="${mount_parts[1]:-}"
             local c_mode="${mount_parts[2]:-ro}"
             if [[ -n "$c_host" ]] && [[ -n "$c_container" ]]; then
-                c_host=$(eval echo "$c_host" 2>/dev/null || echo "$c_host")
+                # Safe tilde expansion (no eval)
+                if [[ "$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)"

package/dashboard/__init__.py

@@ -7,7 +7,7 @@ Modules:
     control: Session control API (start/stop/pause/resume)
 """
 
-__version__ = "6.2.0"
+__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:** v6.2.0
+**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__ = '6.2.0'
+__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": "6.2.0",
+  "version": "6.2.1",
   "description": "Loki Mode by Autonomi - Multi-agent autonomous startup system for Claude Code, Codex CLI, and Gemini CLI",
   "keywords": [
     "agent",