loki-mode 6.4.0 → 6.5.0

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: v6.2.1**
+**Current Version: v6.5.0**
 
 ---
 

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 v6.4.0
+# Loki Mode v6.5.0
 
 **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 |
 
-**v6.4.0 | [Autonomi](https://www.autonomi.dev/) flagship product | ~260 lines core**
+**v6.5.0 | [Autonomi](https://www.autonomi.dev/) flagship product | ~260 lines core**

package/VERSION

@@ -1 +1 @@
-6.4.0
+6.5.0

package/autonomy/hooks/migration-hooks.sh

@@ -52,7 +52,7 @@ load_migration_hook_config() {
         # Parse YAML config safely using read/declare instead of eval
         while IFS='=' read -r key val; do
             case "$key" in
-                HOOK_*) declare -g "$key=$val" ;;
+                HOOK_*) printf -v "$key" '%s' "$val" ;;
             esac
         done < <(python3 -c "
 import sys
@@ -224,7 +224,7 @@ try:
     print(len([s for s in steps if s.get('status') != 'completed']))
 except: print(-1)
 " 2>/dev/null || echo -1)
-            [[ "$pending" -gt 0 ]] && echo "GATE_BLOCKED: ${pending} steps still pending" && return 1
+            [[ "$pending" -ne 0 ]] && echo "GATE_BLOCKED: ${pending} steps still pending (or plan missing)" && return 1
             ;;
     esac
 
@@ -236,6 +236,10 @@ hook_on_agent_stop() {
     local features_path="${LOKI_FEATURES_PATH:-}"
 
     [[ "$HOOK_ON_AGENT_STOP_ENABLED" != "true" ]] && return 0
+    if [[ -z "$features_path" ]]; then
+        echo "HOOK_BLOCKED: LOKI_FEATURES_PATH not set. Cannot verify features."
+        return 1
+    fi
     [[ ! -f "$features_path" ]] && return 0
 
     local failing

package/autonomy/loki

@@ -1356,7 +1356,7 @@ cmd_status() {
         [ -n "$line" ] && running_sessions+=("$line")
     done < <(list_running_sessions 2>/dev/null)
 
-    if [ ${#running_sessions[@]} -gt 1 ]; then
+    if [ ${#running_sessions[@]} -gt 0 ]; then
         echo -e "${GREEN}Active Sessions: ${#running_sessions[@]}${NC}"
         for entry in "${running_sessions[@]}"; do
             local sid="${entry%%:*}"
@@ -2092,7 +2092,7 @@ cmd_dashboard_stop() {
         local wait_count=0
         while kill -0 "$pid" 2>/dev/null && [ $wait_count -lt 10 ]; do
             sleep 0.5
-            ((wait_count++))
+            wait_count=$((wait_count + 1))
         done
 
         # Force kill if still running
@@ -2874,20 +2874,17 @@ cmd_run() {
             --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
                 ;;
             -*)
@@ -2904,6 +2901,11 @@ cmd_run() {
         esac
     done
 
+    # Add --parallel once if worktree mode is enabled (not per-flag)
+    if $use_worktree; then
+        start_args+=("--parallel")
+    fi
+
     if [[ -z "$issue_ref" ]]; then
         echo -e "${RED}Error: Issue reference required${NC}"
         echo ""
@@ -2971,6 +2973,13 @@ cmd_run() {
 
     # Detached mode: fork to background
     if $run_detached; then
+        # Guard: prevent launching duplicate session
+        if is_session_running "$session_id"; then
+            echo -e "${RED}Error: Session '$session_id' is already running.${NC}"
+            echo -e "Stop it first with: ${CYAN}loki stop $session_id${NC}"
+            exit 1
+        fi
+
         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}"
@@ -2985,32 +2994,51 @@ cmd_run() {
             branch_name="issue/detach-$(date +%s)"
         fi
 
-        nohup bash -c "
-            cd $(pwd)
-            export LOKI_DETACHED=true
-            export LOKI_PARALLEL_MODE=true
-            export LOKI_SESSION_ID=\"$session_id\"
-            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
-        " > "$log_file" 2>&1 &
+        # Write a temp script to avoid shell injection via variable interpolation
+        local run_script="$LOKI_DIR/scripts/run-${number:-detached}.sh"
+        mkdir -p "$LOKI_DIR/scripts"
+        local loki_cmd
+        loki_cmd="$(command -v loki || echo "$0")"
+        cat > "$run_script" << 'INNER_SCRIPT_EOF'
+#!/usr/bin/env bash
+set -euo pipefail
+cd "$LOKI_RUN_DIR"
+export LOKI_DETACHED=true
+export LOKI_PARALLEL_MODE=true
+"$LOKI_CMD" start "$LOKI_PRD_PATH" ${LOKI_START_ARGS:-}
+
+# Post-completion: create PR if requested
+if [[ "$LOKI_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 "$branch_current" 2>/dev/null || true
+        gh pr create --title "$LOKI_PR_TITLE" --body "Implemented by Loki Mode" --head "$branch_current" 2>/dev/null || true
+    fi
+fi
+# Post-completion: auto-merge if requested
+if [[ "$LOKI_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 "${LOKI_ISSUE_NUMBER:-}" ]]; then
+            gh issue close "$LOKI_ISSUE_NUMBER" --comment "Resolved by Loki Mode" 2>/dev/null || true
+        fi
+    fi
+fi
+INNER_SCRIPT_EOF
+        chmod +x "$run_script"
+
+        # Pass all variables safely via environment
+        LOKI_RUN_DIR="$(pwd)" \
+        LOKI_CMD="$loki_cmd" \
+        LOKI_SESSION_ID="$session_id" \
+        LOKI_WORKTREE_BRANCH="$branch_name" \
+        LOKI_PRD_PATH="$detach_prd" \
+        LOKI_START_ARGS="${start_args[*]+"${start_args[*]}"}" \
+        LOKI_CREATE_PR="$create_pr" \
+        LOKI_AUTO_MERGE="$auto_merge" \
+        LOKI_PR_TITLE="${title:-Implementation for issue ${issue_ref}}" \
+        LOKI_ISSUE_NUMBER="${number:-}" \
+        nohup bash "$run_script" > "$log_file" 2>&1 &
 
         local bg_pid=$!
         echo "$bg_pid" > "$LOKI_DIR/run-${number:-detached}.pid"
@@ -4946,7 +4974,7 @@ cmd_notify_test() {
             echo -n "  Slack...    "
             if send_slack_notification "$message" "Test"; then
                 echo -e "${GREEN}OK${NC}"
-                ((channels_notified++))
+                channels_notified=$((channels_notified + 1))
             else
                 echo -e "${RED}FAILED${NC}"
             fi
@@ -4959,7 +4987,7 @@ cmd_notify_test() {
             echo -n "  Discord...  "
             if send_discord_notification "$message" "Test"; then
                 echo -e "${GREEN}OK${NC}"
-                ((channels_notified++))
+                channels_notified=$((channels_notified + 1))
             else
                 echo -e "${RED}FAILED${NC}"
             fi
@@ -4972,7 +5000,7 @@ cmd_notify_test() {
             echo -n "  Webhook...  "
             if send_webhook_notification "$message" "Test"; then
                 echo -e "${GREEN}OK${NC}"
-                ((channels_notified++))
+                channels_notified=$((channels_notified + 1))
             else
                 echo -e "${RED}FAILED${NC}"
             fi
@@ -6691,7 +6719,7 @@ Tasks:
             local provider_name="${LOKI_PROVIDER:-claude}"
             case "$provider_name" in
                 claude)
-                    (cd "$codebase_path" && claude --dangerously-skip-permissions -p "$phase_prompt" --output-format stream-json --verbose 2>&1) | \
+                    { (cd "$codebase_path" && claude --dangerously-skip-permissions -p "$phase_prompt" --output-format stream-json --verbose 2>&1) | \
                         while IFS= read -r line; do
                             # Extract text from stream-json
                             if echo "$line" | python3 -c "
@@ -6706,8 +6734,7 @@ except Exception: pass
 " 2>/dev/null; then
                                 true
                             fi
-                        done
-                    phase_exit=${PIPESTATUS[0]}
+                        done; } && phase_exit=0 || phase_exit=$?
                     ;;
                 codex)
                     (cd "$codebase_path" && codex exec --full-auto "$phase_prompt" 2>&1) || phase_exit=$?
@@ -6854,7 +6881,7 @@ IMPORTANT RULES:
         local provider_name="${LOKI_PROVIDER:-claude}"
         case "$provider_name" in
             claude)
-                (cd "$codebase_path" && claude --dangerously-skip-permissions -p "$doc_prompt" --output-format stream-json --verbose 2>&1) | \
+                { (cd "$codebase_path" && claude --dangerously-skip-permissions -p "$doc_prompt" --output-format stream-json --verbose 2>&1) | \
                     while IFS= read -r line; do
                         if echo "$line" | python3 -c "
 import sys, json
@@ -6868,8 +6895,7 @@ except Exception: pass
 " 2>/dev/null; then
                             true
                         fi
-                    done
-                doc_exit=${PIPESTATUS[0]}
+                    done; } && doc_exit=0 || doc_exit=$?
                 ;;
             codex)
                 (cd "$codebase_path" && codex exec --full-auto "$doc_prompt" 2>&1) || doc_exit=$?

package/autonomy/run.sh

@@ -7434,12 +7434,13 @@ run_autonomous() {
         audit_agent_action "cli_invoke" "Starting iteration $ITERATION_COUNT" "provider=${PROVIDER_NAME:-claude},tier=$CURRENT_TIER"
 
         # Provider-specific invocation with dynamic tier selection
+        local exit_code=0
         case "${PROVIDER_NAME:-claude}" in
             claude)
                 # Claude: Full features with stream-json output and agent tracking
                 # Uses dynamic tier for model selection based on RARV phase
                 # Pass tier to Python via environment for dashboard display
-                LOKI_CURRENT_MODEL="$tier_param" \
+                { LOKI_CURRENT_MODEL="$tier_param" \
                 claude --dangerously-skip-permissions --model "$tier_param" -p "$prompt" \
             --output-format stream-json --verbose 2>&1 | \
             tee -a "$log_file" "$agent_log" | \
@@ -7647,7 +7648,7 @@ if __name__ == "__main__":
     except BrokenPipeError:
         sys.exit(0)
 '
-                local exit_code=${PIPESTATUS[0]}
+                } && exit_code=0 || exit_code=$?
                 ;;
 
             codex)
@@ -7655,10 +7656,10 @@ if __name__ == "__main__":
                 # Uses positional prompt after exec subcommand
                 # Note: Effort is set via env var, not CLI flag
                 # Uses dynamic tier from RARV phase (tier_param already set above)
-                CODEX_MODEL_REASONING_EFFORT="$tier_param" \
+                { CODEX_MODEL_REASONING_EFFORT="$tier_param" \
                 codex exec --full-auto \
-                    "$prompt" 2>&1 | tee -a "$log_file" "$agent_log"
-                local exit_code=${PIPESTATUS[0]}
+                    "$prompt" 2>&1 | tee -a "$log_file" "$agent_log"; \
+                } && exit_code=0 || exit_code=$?
                 ;;
 
             gemini)
@@ -7672,8 +7673,8 @@ if __name__ == "__main__":
                 # Try primary model, fallback on rate limit
                 local tmp_output
                 tmp_output=$(mktemp)
-                gemini --approval-mode=yolo --model "$model" "$prompt" < /dev/null 2>&1 | tee "$tmp_output" | tee -a "$log_file" "$agent_log"
-                local exit_code=${PIPESTATUS[0]}
+                { gemini --approval-mode=yolo --model "$model" "$prompt" < /dev/null 2>&1 | tee "$tmp_output" | tee -a "$log_file" "$agent_log"; \
+                } && exit_code=0 || exit_code=$?
 
                 if [[ $exit_code -ne 0 ]] && grep -qiE "(rate.?limit|429|quota|resource.?exhausted)" "$tmp_output"; then
                     log_warn "Rate limit hit on $model, falling back to $fallback"
@@ -8143,17 +8144,18 @@ except (json.JSONDecodeError, OSError): pass
         stop_dashboard
         stop_status_monitor
         kill_all_registered
-        rm -f .loki/loki.pid .loki/PAUSE 2>/dev/null
+        rm -f "$loki_dir/loki.pid" "$loki_dir/PAUSE" 2>/dev/null
         # Clean up per-session PID file if running with session ID
         if [ -n "${LOKI_SESSION_ID:-}" ]; then
-            rm -f ".loki/sessions/${LOKI_SESSION_ID}/loki.pid" 2>/dev/null
+            rm -f "$loki_dir/sessions/${LOKI_SESSION_ID}/loki.pid" 2>/dev/null
         fi
         # Mark session.json as stopped
-        if [ -f ".loki/session.json" ]; then
-            python3 -c "
-import json
+        if [ -f "$loki_dir/session.json" ]; then
+            _LOKI_SESSION_FILE="$loki_dir/session.json" python3 -c "
+import json, os
+sf = os.environ['_LOKI_SESSION_FILE']
 try:
-    with open('.loki/session.json', 'r+') as f:
+    with open(sf, 'r+') as f:
         d = json.load(f); d['status'] = 'stopped'
         f.seek(0); f.truncate(); json.dump(d, f)
 except (json.JSONDecodeError, OSError): pass
@@ -8736,17 +8738,19 @@ main() {
     fi
     stop_dashboard
     stop_status_monitor
-    rm -f .loki/loki.pid 2>/dev/null
+    local loki_dir="${TARGET_DIR:-.}/.loki"
+    rm -f "$loki_dir/loki.pid" 2>/dev/null
     # Clean up per-session PID file if running with session ID
     if [ -n "${LOKI_SESSION_ID:-}" ]; then
-        rm -f ".loki/sessions/${LOKI_SESSION_ID}/loki.pid" 2>/dev/null
+        rm -f "$loki_dir/sessions/${LOKI_SESSION_ID}/loki.pid" 2>/dev/null
     fi
     # Mark session.json as stopped
-    if [ -f ".loki/session.json" ]; then
-        python3 -c "
-import json
+    if [ -f "$loki_dir/session.json" ]; then
+        _LOKI_SESSION_FILE="$loki_dir/session.json" python3 -c "
+import json, os
+sf = os.environ['_LOKI_SESSION_FILE']
 try:
-    with open('.loki/session.json', 'r+') as f:
+    with open(sf, 'r+') as f:
         d = json.load(f); d['status'] = 'stopped'
         f.seek(0); f.truncate(); json.dump(d, f)
 except (json.JSONDecodeError, OSError): pass

package/autonomy/sandbox.sh

@@ -68,28 +68,32 @@ PROMPT_INJECTION_ENABLED="${LOKI_PROMPT_INJECTION:-false}"
 
 # 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"
-)
+# Uses functions instead of declare -A for bash 3.2 compatibility (macOS default)
+_get_mount_preset() {
+    case "$1" in
+        gh)        echo "$HOME/.config/gh:/home/loki/.config/gh:ro" ;;
+        git)       echo "$HOME/.gitconfig:/home/loki/.gitconfig:ro" ;;
+        ssh)       echo "$HOME/.ssh/known_hosts:/home/loki/.ssh/known_hosts:ro" ;;
+        aws)       echo "$HOME/.aws:/home/loki/.aws:ro" ;;
+        azure)     echo "$HOME/.azure:/home/loki/.azure:ro" ;;
+        kube)      echo "$HOME/.kube:/home/loki/.kube:ro" ;;
+        terraform) echo "$HOME/.terraform.d:/home/loki/.terraform.d:ro" ;;
+        gcloud)    echo "$HOME/.config/gcloud:/home/loki/.config/gcloud:ro" ;;
+        npm)       echo "$HOME/.npmrc:/home/loki/.npmrc:ro" ;;
+        *)         echo "" ;;
+    esac
+}
 
 # 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_*"
-)
+_get_env_preset() {
+    case "$1" in
+        aws)       echo "AWS_REGION,AWS_PROFILE,AWS_DEFAULT_REGION" ;;
+        azure)     echo "AZURE_SUBSCRIPTION_ID,AZURE_TENANT_ID" ;;
+        gcloud)    echo "GOOGLE_PROJECT,GOOGLE_REGION,GCLOUD_PROJECT" ;;
+        terraform) echo "TF_VAR_*" ;;
+        *)         echo "" ;;
+    esac
+}
 
 #===============================================================================
 # Utility Functions
@@ -836,7 +840,8 @@ except: pass
         while IFS= read -r name; do
             [[ -z "$name" ]] && continue
 
-            local preset_value="${DOCKER_MOUNT_PRESETS[$name]:-}"
+            local preset_value
+            preset_value="$(_get_mount_preset "$name")"
             if [[ -z "$preset_value" ]]; then
                 log_warn "Unknown Docker mount preset: $name"
                 continue
@@ -861,7 +866,8 @@ except: pass
             fi
 
             # Add associated env vars
-            local env_list="${DOCKER_ENV_PRESETS[$name]:-}"
+            local env_list
+            env_list="$(_get_env_preset "$name")"
             if [[ -n "$env_list" ]]; then
                 IFS=',' read -ra env_names <<< "$env_list"
                 local env_name

package/autonomy/telemetry.sh

@@ -52,17 +52,30 @@ loki_telemetry() {
     os_name=$(uname -s 2>/dev/null || echo "unknown")
     arch=$(uname -m 2>/dev/null || echo "unknown")
 
-    # Build properties from remaining args (key=value pairs)
-    local extra_props=""
+    # Build JSON payload safely using Python to prevent injection
+    local extra_args=""
     for arg in "$@"; do
-        local key="${arg%%=*}"
-        local val="${arg#*=}"
-        extra_props="${extra_props},\"${key}\":\"${val}\""
+        extra_args="${extra_args}${extra_args:+ }${arg}"
     done
 
     local payload
-    payload=$(printf '{"api_key":"%s","event":"%s","distinct_id":"%s","properties":{"os":"%s","arch":"%s","version":"%s","channel":"%s"%s}}' \
-        "$LOKI_POSTHOG_KEY" "$event" "$distinct_id" "$os_name" "$arch" "$version" "$channel" "$extra_props")
+    payload=$(python3 -c "
+import json, sys
+props = {'os': sys.argv[1], 'arch': sys.argv[2], 'version': sys.argv[3], 'channel': sys.argv[4]}
+for arg in sys.argv[5:]:
+    if '=' in arg:
+        k, v = arg.split('=', 1)
+        props[k] = v
+print(json.dumps({'api_key': '$LOKI_POSTHOG_KEY', 'event': sys.argv[5] if len(sys.argv) > 5 else '', 'distinct_id': '$distinct_id', 'properties': props}))
+" "$os_name" "$arch" "$version" "$channel" $extra_args 2>/dev/null) || return 0
+    # Re-inject event and distinct_id properly
+    payload=$(python3 -c "
+import json, sys
+d = json.loads(sys.argv[1])
+d['event'] = sys.argv[2]
+d['distinct_id'] = sys.argv[3]
+print(json.dumps(d))
+" "$payload" "$event" "$distinct_id" 2>/dev/null) || return 0
 
     (curl -sS --max-time 3 -X POST "${LOKI_POSTHOG_HOST}/capture/" \
         -H "Content-Type: application/json" \

package/dashboard/__init__.py

@@ -7,7 +7,7 @@ Modules:
     control: Session control API (start/stop/pause/resume)
 """
 
-__version__ = "6.4.0"
+__version__ = "6.5.0"
 
 # Expose the control app for easy import
 try:

package/dashboard/migration_engine.py

@@ -886,7 +886,7 @@ Summary: {summary}
             if len(entries) > 50:
                 header = entries[0]
                 recent = entries[-50:]
-                content = header + "\n## Session:".join(recent)
+                content = header + "\n## Session:" + "\n## Session:".join(recent)
             else:
                 content = existing
             content += entry

package/dashboard/server.py

@@ -536,9 +536,13 @@ async def get_status() -> StatusResponse:
 
     # Global session
     if running:
+        try:
+            _global_pid = int(pid_str) if pid_str else 0
+        except (ValueError, TypeError):
+            _global_pid = 0
         active_session_list.append(SessionInfo(
             session_id="global",
-            pid=int(pid_str) if pid_str else 0,
+            pid=_global_pid,
             status=status,
         ))
 
@@ -1441,7 +1445,7 @@ async def query_audit_logs(
     action: Optional[str] = None,
     resource_type: Optional[str] = None,
     resource_id: Optional[str] = None,
-    limit: int = 100,
+    limit: int = Query(default=100, ge=1, le=1000),
     offset: int = 0,
 ):
     """
@@ -1561,7 +1565,7 @@ async def get_memory_summary():
 
 
 @app.get("/api/memory/episodes")
-async def list_episodes(limit: int = 50):
+async def list_episodes(limit: int = Query(default=50, ge=1, le=1000)):
     """List episodic memory entries."""
     ep_dir = _get_loki_dir() / "memory" / "episodic"
     episodes = []
@@ -1578,11 +1582,15 @@ async def list_episodes(limit: int = 50):
 @app.get("/api/memory/episodes/{episode_id}")
 async def get_episode(episode_id: str):
     """Get a specific episodic memory entry."""
-    ep_dir = _get_loki_dir() / "memory" / "episodic"
+    loki_dir = _get_loki_dir()
+    ep_dir = loki_dir / "memory" / "episodic"
     if not ep_dir.exists():
         raise HTTPException(status_code=404, detail="Episode not found")
     # Try direct filename match
     for f in ep_dir.glob("*.json"):
+        resolved = os.path.realpath(f)
+        if not resolved.startswith(os.path.realpath(str(loki_dir))):
+            raise HTTPException(status_code=403, detail="Access denied")
         try:
             data = json.loads(f.read_text())
             if data.get("id") == episode_id or f.stem == episode_id:
@@ -1633,10 +1641,14 @@ async def list_skills():
 @app.get("/api/memory/skills/{skill_id}")
 async def get_skill(skill_id: str):
     """Get a specific procedural skill."""
-    skills_dir = _get_loki_dir() / "memory" / "skills"
+    loki_dir = _get_loki_dir()
+    skills_dir = loki_dir / "memory" / "skills"
     if not skills_dir.exists():
         raise HTTPException(status_code=404, detail="Skill not found")
     for f in skills_dir.glob("*.json"):
+        resolved = os.path.realpath(f)
+        if not resolved.startswith(os.path.realpath(str(loki_dir))):
+            raise HTTPException(status_code=403, detail="Access denied")
         try:
             data = json.loads(f.read_text())
             if data.get("id") == skill_id or f.stem == skill_id:
@@ -1706,6 +1718,7 @@ def _read_learning_signals(signal_type: Optional[str] = None, limit: int = 50) -
     (learning/emitter.py). Each file contains a single signal object with fields:
     id, type, source, action, timestamp, confidence, outcome, data, context.
     """
+    limit = min(limit, 1000)
     signals_dir = _get_loki_dir() / "learning" / "signals"
     if not signals_dir.exists() or not signals_dir.is_dir():
         return []
@@ -1825,7 +1838,7 @@ async def get_learning_signals(
     timeRange: str = "7d",
     signalType: Optional[str] = None,
     source: Optional[str] = None,
-    limit: int = 50,
+    limit: int = Query(default=50, ge=1, le=1000),
     offset: int = 0,
 ):
     """Get raw learning signals from both events.jsonl and learning signals directory."""
@@ -2030,7 +2043,7 @@ async def trigger_aggregation():
 
 
 @app.get("/api/learning/preferences")
-async def get_learning_preferences(limit: int = 50):
+async def get_learning_preferences(limit: int = Query(default=50, ge=1, le=1000)):
     """Get aggregated user preferences from events and learning signals directory."""
     events = _read_events("30d")
     prefs = [e for e in events if e.get("type") == "user_preference"]
@@ -2042,7 +2055,7 @@ async def get_learning_preferences(limit: int = 50):
 
 
 @app.get("/api/learning/errors")
-async def get_learning_errors(limit: int = 50):
+async def get_learning_errors(limit: int = Query(default=50, ge=1, le=1000)):
     """Get aggregated error patterns from events and learning signals directory."""
     events = _read_events("30d")
     errors = [e for e in events if e.get("type") == "error_pattern"]
@@ -2054,7 +2067,7 @@ async def get_learning_errors(limit: int = 50):
 
 
 @app.get("/api/learning/success")
-async def get_learning_success(limit: int = 50):
+async def get_learning_success(limit: int = Query(default=50, ge=1, le=1000)):
     """Get aggregated success patterns from events and learning signals directory."""
     events = _read_events("30d")
     successes = [e for e in events if e.get("type") == "success_pattern"]
@@ -2066,7 +2079,7 @@ async def get_learning_success(limit: int = 50):
 
 
 @app.get("/api/learning/tools")
-async def get_tool_efficiency(limit: int = 50):
+async def get_tool_efficiency(limit: int = Query(default=50, ge=1, le=1000)):
     """Get tool efficiency rankings from events and learning signals directory."""
     events = _read_events("30d")
     tools = [e for e in events if e.get("type") == "tool_efficiency"]
@@ -2505,7 +2518,7 @@ async def get_council_state():
 
 
 @app.get("/api/council/verdicts")
-async def get_council_verdicts(limit: int = 20):
+async def get_council_verdicts(limit: int = Query(default=20, ge=1, le=1000)):
     """Get council vote history (decision log)."""
     state_file = _get_loki_dir() / "council" / "state.json"
     verdicts = []

package/docs/INSTALLATION.md

@@ -2,11 +2,11 @@
 
 The flagship product of [Autonomi](https://www.autonomi.dev/). Complete installation instructions for all platforms and use cases.
 
-**Version:** v6.4.0
+**Version:** v6.5.0
 
 ---
 
-## What's New in v6.4.0
+## What's New in v6.5.0
 
 ### Dual-Mode Architecture (v6.0.0)
 - `loki run` command for direct autonomous execution

package/events/emit.sh

@@ -43,7 +43,7 @@ fi
 
 # JSON escape helper: handles \, ", and control characters
 json_escape() {
-    printf '%s' "$1" | sed 's/\\/\\\\/g; s/"/\\"/g; s/\t/\\t/g; s/\r/\\r/g' | tr -d '\n'
+    printf '%s' "$1" | sed 's/\\/\\\\/g; s/"/\\"/g; s/\t/\\t/g; s/\r/\\r/g' | awk '{if(NR>1) printf "\\n"; printf "%s", $0}'
 }
 
 # Build payload JSON

package/mcp/__init__.py

@@ -57,4 +57,4 @@ try:
 except ImportError:
     __all__ = ['mcp']
 
-__version__ = '6.4.0'
+__version__ = '6.5.0'

package/mcp/server.py

@@ -20,6 +20,7 @@ import os
 import json
 import logging
 import threading
+import uuid
 from datetime import datetime, timezone
 from typing import Optional, List, Dict, Any
 
@@ -563,11 +564,11 @@ async def loki_memory_store_pattern(
         from memory.schemas import SemanticPattern
 
         base_path = safe_path_join('.loki', 'memory')
-        engine = MemoryEngine(base_path)
+        engine = MemoryEngine(base_path=base_path)
         engine.initialize()
 
         pattern_obj = SemanticPattern(
-            id=f"pattern-{datetime.now(timezone.utc).strftime('%Y%m%d%H%M%S')}",
+            id=f"pattern-{datetime.now(timezone.utc).strftime('%Y%m%d%H%M%S')}-{uuid.uuid4().hex[:8]}",
             pattern=pattern,
             category=category,
             conditions=[],
@@ -821,7 +822,7 @@ async def loki_state_get() -> str:
         try:
             from memory.engine import MemoryEngine
             memory_path = safe_path_join('.loki', 'memory')
-            engine = MemoryEngine(memory_path)
+            engine = MemoryEngine(base_path=memory_path)
             state["memory_stats"] = engine.get_stats()
         except Exception:
             state["memory_stats"] = None
@@ -1004,9 +1005,13 @@ async def loki_start_project(prd_content: str = "", prd_path: str = "") -> str:
     try:
         content = prd_content
         if not content and prd_path:
-            resolved = safe_path_join('.', prd_path)
-            if os.path.exists(resolved):
-                with safe_open(resolved, 'r') as f:
+            # Resolve relative paths against project root, absolute paths used as-is
+            if os.path.isabs(prd_path):
+                resolved = os.path.realpath(prd_path)
+            else:
+                resolved = os.path.realpath(os.path.join(get_project_root(), prd_path))
+            if os.path.exists(resolved) and os.path.isfile(resolved):
+                with open(resolved, 'r', encoding='utf-8') as f:
                     content = f.read()
             else:
                 return json.dumps({"error": f"PRD file not found: {prd_path}"})

package/memory/embeddings.py

@@ -307,6 +307,10 @@ class TextChunker:
         if len(text) <= max_size:
             return [text]
 
+        # Guard against infinite loop when overlap >= max_size
+        if overlap >= max_size:
+            overlap = 0
+
         chunks = []
         start = 0
         while start < len(text):
@@ -1062,12 +1066,17 @@ class EmbeddingEngine:
         # Find texts that need computing
         texts_to_compute = []
         indices_to_compute = []
-        for i, (text, key) in enumerate(zip(texts, cache_keys)):
-            if not self.config.cache_enabled or cached_results.get(key) is None:
-                texts_to_compute.append(text)
-                indices_to_compute.append(i)
-            else:
-                self._metrics["cache_hits"] += 1
+        if not self.config.cache_enabled:
+            # No cache - all texts need computing
+            texts_to_compute = list(texts)
+            indices_to_compute = list(range(len(texts)))
+        else:
+            for i, (text, key) in enumerate(zip(texts, cache_keys)):
+                if cached_results.get(key) is None:
+                    texts_to_compute.append(text)
+                    indices_to_compute.append(i)
+                else:
+                    self._metrics["cache_hits"] += 1
 
         # Compute missing embeddings
         new_embeddings = None

package/memory/engine.py

@@ -881,6 +881,21 @@ class MemoryEngine:
             for e in errors_raw
         ]
 
+        # Parse last_accessed datetime
+        last_accessed = None
+        last_accessed_raw = data.get("last_accessed")
+        if last_accessed_raw:
+            if isinstance(last_accessed_raw, str):
+                if last_accessed_raw.endswith("Z"):
+                    last_accessed_raw = last_accessed_raw[:-1]
+                last_accessed = datetime.fromisoformat(last_accessed_raw)
+                if last_accessed.tzinfo is None:
+                    last_accessed = last_accessed.replace(tzinfo=timezone.utc)
+            elif isinstance(last_accessed_raw, datetime):
+                last_accessed = last_accessed_raw
+                if last_accessed.tzinfo is None:
+                    last_accessed = last_accessed.replace(tzinfo=timezone.utc)
+
         return EpisodeTrace(
             id=data.get("id", ""),
             task_id=data.get("task_id", ""),
@@ -897,6 +912,9 @@ class MemoryEngine:
             tokens_used=data.get("tokens_used", 0),
             files_read=data.get("files_read", context.get("files_involved", [])),
             files_modified=data.get("files_modified", []),
+            importance=data.get("importance", 0.5),
+            last_accessed=last_accessed,
+            access_count=data.get("access_count", 0),
         )
 
     def _dict_to_pattern(self, data: Dict[str, Any]) -> SemanticPattern:
@@ -924,6 +942,21 @@ class MemoryEngine:
             for link in links_raw
         ]
 
+        # Parse last_accessed datetime
+        last_accessed = None
+        last_accessed_raw = data.get("last_accessed")
+        if last_accessed_raw:
+            if isinstance(last_accessed_raw, str):
+                if last_accessed_raw.endswith("Z"):
+                    last_accessed_raw = last_accessed_raw[:-1]
+                last_accessed = datetime.fromisoformat(last_accessed_raw)
+                if last_accessed.tzinfo is None:
+                    last_accessed = last_accessed.replace(tzinfo=timezone.utc)
+            elif isinstance(last_accessed_raw, datetime):
+                last_accessed = last_accessed_raw
+                if last_accessed.tzinfo is None:
+                    last_accessed = last_accessed.replace(tzinfo=timezone.utc)
+
         return SemanticPattern(
             id=data.get("id", ""),
             pattern=data.get("pattern", ""),
@@ -936,6 +969,9 @@ class MemoryEngine:
             usage_count=data.get("usage_count", 0),
             last_used=last_used,
             links=links,
+            importance=data.get("importance", 0.5),
+            last_accessed=last_accessed,
+            access_count=data.get("access_count", 0),
         )
 
     def _dict_to_skill(self, data: Dict[str, Any]) -> ProceduralSkill:
@@ -945,6 +981,22 @@ class MemoryEngine:
             ErrorFix.from_dict(e) if isinstance(e, dict) else e
             for e in raw_errors
         ]
+
+        # Parse last_accessed datetime
+        last_accessed = None
+        last_accessed_raw = data.get("last_accessed")
+        if last_accessed_raw:
+            if isinstance(last_accessed_raw, str):
+                if last_accessed_raw.endswith("Z"):
+                    last_accessed_raw = last_accessed_raw[:-1]
+                last_accessed = datetime.fromisoformat(last_accessed_raw)
+                if last_accessed.tzinfo is None:
+                    last_accessed = last_accessed.replace(tzinfo=timezone.utc)
+            elif isinstance(last_accessed_raw, datetime):
+                last_accessed = last_accessed_raw
+                if last_accessed.tzinfo is None:
+                    last_accessed = last_accessed.replace(tzinfo=timezone.utc)
+
         return ProceduralSkill(
             id=data.get("id", ""),
             name=data.get("name", ""),
@@ -953,6 +1005,10 @@ class MemoryEngine:
             steps=data.get("steps", []),
             common_errors=common_errors,
             exit_criteria=data.get("exit_criteria", []),
+            example_usage=data.get("example_usage"),
+            importance=data.get("importance", 0.5),
+            last_accessed=last_accessed,
+            access_count=data.get("access_count", 0),
         )
 
     def _skill_to_markdown(self, skill: Dict[str, Any]) -> str:

package/memory/schemas.py

@@ -20,9 +20,13 @@ from typing import Optional, List, Dict, Any
 def _to_utc_isoformat(dt: datetime) -> str:
     """Convert datetime to UTC ISO 8601 string with Z suffix.
 
-    Handles both timezone-aware and timezone-naive datetimes,
-    and avoids double-suffixing if already has timezone info.
+    Handles both timezone-aware and timezone-naive datetimes.
+    If dt has a non-UTC timezone, converts to UTC first.
     """
+    # If timezone-aware and not UTC, convert to UTC
+    if dt.tzinfo is not None and dt.utcoffset() != timezone.utc.utcoffset(None):
+        dt = dt.astimezone(timezone.utc)
+
     iso = dt.isoformat()
     # If already has timezone offset like +00:00, replace with Z
     if iso.endswith("+00:00"):

package/memory/storage.py

@@ -233,7 +233,7 @@ class MemoryStorage:
             path: Path to JSON file
 
         Returns:
-            Parsed JSON as dictionary, or None if file doesn't exist
+            Parsed JSON as dictionary, or None if file doesn't exist or is corrupted
         """
         path = Path(path)
         if not path.exists():
@@ -241,7 +241,10 @@ class MemoryStorage:
 
         with self._file_lock(path, exclusive=False):
             with open(path, "r") as f:
-                return json.load(f)
+                try:
+                    return json.load(f)
+                except json.JSONDecodeError:
+                    return None
 
     def _generate_id(self, prefix: str) -> str:
         """

package/memory/token_economics.py

@@ -505,9 +505,12 @@ class TokenEconomics:
             Ratio of discovery_tokens / read_tokens (0.0 if no reads)
         """
         read_tokens = self.metrics["read_tokens"]
+        discovery_tokens = self.metrics["discovery_tokens"]
         if read_tokens == 0:
+            if discovery_tokens > 0:
+                return 999.99  # Sentinel: all discovery, no productive reads
             return 0.0
-        return self.metrics["discovery_tokens"] / read_tokens
+        return discovery_tokens / read_tokens
 
     def get_savings_percent(self) -> float:
         """

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "loki-mode",
-  "version": "6.4.0",
+  "version": "6.5.0",
   "description": "Loki Mode by Autonomi - Multi-agent autonomous startup system for Claude Code, Codex CLI, and Gemini CLI",
   "keywords": [
     "agent",