aether-colony 5.1.0 → 5.3.0

package/.aether/aether-utils.sh

@@ -44,6 +44,10 @@ CURRENT_LOCK=${CURRENT_LOCK:-""}
 [[ -f "$SCRIPT_DIR/utils/pheromone.sh" ]] && source "$SCRIPT_DIR/utils/pheromone.sh"
 [[ -f "$SCRIPT_DIR/utils/scan.sh" ]] && source "$SCRIPT_DIR/utils/scan.sh"
 [[ -f "$SCRIPT_DIR/utils/emoji-audit.sh" ]] && source "$SCRIPT_DIR/utils/emoji-audit.sh"
+[[ -f "$SCRIPT_DIR/utils/immune.sh" ]] && source "$SCRIPT_DIR/utils/immune.sh"
+[[ -f "$SCRIPT_DIR/utils/council.sh" ]] && source "$SCRIPT_DIR/utils/council.sh"
+[[ -f "$SCRIPT_DIR/utils/clash-detect.sh" ]] && source "$SCRIPT_DIR/utils/clash-detect.sh"
+[[ -f "$SCRIPT_DIR/utils/worktree.sh" ]] && source "$SCRIPT_DIR/utils/worktree.sh"
 
 # Fallback error constants if error-handler.sh wasn't sourced
 # This prevents "unbound variable" errors in older installations
@@ -106,7 +110,7 @@ if ! type json_err &>/dev/null; then
     local code="${1:-E_UNKNOWN}"
     local message="${2:-An unknown error occurred}"
     printf '[aether] Warning: error-handler.sh not loaded — using minimal fallback\n' >&2
-    printf '{"ok":false,"error":{"code":"%s","message":"%s"}}\n' "$code" "$message" >&2
+    printf '%s\n' "$(jq -nc --arg c "$code" --arg m "$message" '{ok:false,error:{code:$c,message:$m}}')" >&2
     exit 1
   }
 fi
@@ -570,7 +574,7 @@ Git Commits:  0
 
 **Colony Memory Active** 🧠🐜
 EOF
-      json_ok "{\"updated\":true,\"action\":\"init\",\"file\":\"$ctx_file\"}"
+      json_ok "$(jq -nc --arg file "$ctx_file" '{updated:true,action:"init",file:$file}')"
       ;;
 
     update-phase)
@@ -586,7 +590,7 @@ EOF
       sed -i.bak "s/| \*\*Phase Name\*\* | .*/| **Phase Name** | $new_phase_name |/" "$ctx_file" && rm -f "$ctx_file.bak"
       sed -i.bak "s/| \*\*Safe to Clear?\*\* | .*/| **Safe to Clear?** | $safe_clear — $safe_reason |/" "$ctx_file" && rm -f "$ctx_file.bak"
 
-      json_ok "{\"updated\":true,\"action\":\"update-phase\",\"phase\":$new_phase}"
+      json_ok "$(jq -nc --argjson phase "$new_phase" '{updated:true,action:"update-phase",phase:$phase}')"
       ;;
 
     activity)
@@ -613,7 +617,7 @@ EOF
       ' "$ctx_file" > "$ctx_tmp"
 
       mv "$ctx_tmp" "$ctx_file"
-      json_ok "{\"updated\":true,\"action\":\"activity\",\"command\":\"$cmd\"}"
+      json_ok "$(jq -nc --arg cmd "$cmd" '{updated:true,action:"activity",command:$cmd}')"
       ;;
 
     safe-to-clear)
@@ -625,7 +629,7 @@ EOF
       sed -i.bak "s/| \*\*Last Updated\*\* | .*/| **Last Updated** | $ctx_ts |/" "$ctx_file" && rm -f "$ctx_file.bak"
       sed -i.bak "s/| \*\*Safe to Clear?\*\* | .*/| **Safe to Clear?** | $safe — $reason |/" "$ctx_file" && rm -f "$ctx_file.bak"
 
-      json_ok "{\"updated\":true,\"action\":\"safe-to-clear\",\"safe\":\"$safe\"}"
+      json_ok "$(jq -nc --arg safe "$safe" '{updated:true,action:"safe-to-clear",safe:$safe}')"
       ;;
 
     constraint)
@@ -651,7 +655,7 @@ EOF
 }" "$ctx_file" && rm -f "$ctx_file.bak"
       fi
 
-      json_ok "{\"updated\":true,\"action\":\"constraint\",\"type\":\"$c_type\"}"
+      json_ok "$(jq -nc --arg type "$c_type" '{updated:true,action:"constraint",type:$type}')"
       ;;
 
     decision)
@@ -692,7 +696,7 @@ EOF
         --ttl "30d" 2>/dev/null \
         || _aether_log_error "Could not emit feedback signal for decision"  # SUPPRESS:OK -- read-default: returns fallback on failure
 
-      json_ok "{\"updated\":true,\"action\":\"decision\"}"
+      json_ok "$(jq -nc '{updated:true,action:"decision"}')"
       ;;
 
     build-start)
@@ -706,7 +710,7 @@ EOF
       sed -i.bak "s/## 📍 What's In Progress/## 📍 What's In Progress\n\n**Phase $phase_id Build IN PROGRESS**\n- Workers: $worker_count | Tasks: $tasks_count\n- Started: $ctx_ts/" "$ctx_file" && rm -f "$ctx_file.bak"
       sed -i.bak "s/| \*\*Safe to Clear?\*\* | .*/| **Safe to Clear?** | ⚠️ NO — Build in progress |/" "$ctx_file" && rm -f "$ctx_file.bak"
 
-      json_ok "{\"updated\":true,\"action\":\"build-start\",\"workers\":$worker_count}"
+      json_ok "$(jq -nc --argjson workers "$worker_count" '{updated:true,action:"build-start",workers:$workers}')"
       ;;
 
     worker-spawn)
@@ -727,7 +731,7 @@ EOF
         { print }
       ' "$ctx_file" > "$ctx_tmp" && mv "$ctx_tmp" "$ctx_file"
 
-      json_ok "{\"updated\":true,\"action\":\"worker-spawn\",\"ant\":\"$ant_name\"}"
+      json_ok "$(jq -nc --arg ant "$ant_name" '{updated:true,action:"worker-spawn",ant:$ant}')"
       ;;
 
     worker-complete)
@@ -738,7 +742,7 @@ EOF
 
       sed -i.bak "s/- .*$ant_name .*$/- $ant_name: $status (updated $ctx_ts)/" "$ctx_file" && rm -f "$ctx_file.bak"
 
-      json_ok "{\"updated\":true,\"action\":\"worker-complete\",\"ant\":\"$ant_name\"}"
+      json_ok "$(jq -nc --arg ant "$ant_name" '{updated:true,action:"worker-complete",ant:$ant}')"
       ;;
 
     build-progress)
@@ -750,7 +754,7 @@ EOF
 
       sed -i.bak "s/Build IN PROGRESS/Build IN PROGRESS ($percentage% complete)/" "$ctx_file" && rm -f "$ctx_file.bak"
 
-      json_ok "{\"updated\":true,\"action\":\"build-progress\",\"percent\":$percentage}"
+      json_ok "$(jq -nc --argjson percent "$percentage" '{updated:true,action:"build-progress",percent:$percent}')"
       ;;
 
     build-complete)
@@ -776,7 +780,7 @@ EOF
 
       sed -i.bak "s/| \*\*Safe to Clear?\*\* | .*/| **Safe to Clear?** | ✅ YES — Build $status |/" "$ctx_file" && rm -f "$ctx_file.bak"
 
-      json_ok "{\"updated\":true,\"action\":\"build-complete\",\"status\":\"$status\"}"
+      json_ok "$(jq -nc --arg status "$status" '{updated:true,action:"build-complete",status:$status}')"
       ;;
 
     *)
@@ -953,7 +957,7 @@ EOF
   # Atomically replace the file
   mv "$temp_file" "$changelog_file"
 
-  json_ok '{"appended":true,"date":"'"$date_str"'","phase":"'"$phase"'","plan":"'"$plan"'"}'
+  json_ok "$(jq -nc --arg date "$date_str" --arg phase "$phase" --arg plan "$plan" '{appended:true,date:$date,phase:$phase,plan:$plan}')"
 }
 
 # Collect plan data for changelog entry
@@ -1174,7 +1178,7 @@ case "$cmd" in
     cat <<'HELP_EOF'
 {
   "ok": true,
-  "commands": ["help","version","validate-state","validate-oracle-state","load-state","unload-state","error-add","error-pattern-check","error-summary","activity-log","activity-log-init","activity-log-read","learning-promote","learning-inject","learning-observe","learning-check-promotion","learning-promote-auto","memory-capture","queen-thresholds","context-capsule","rolling-summary","generate-ant-name","spawn-log","spawn-complete","spawn-can-spawn","spawn-get-depth","spawn-tree-load","spawn-tree-active","spawn-tree-depth","spawn-efficiency","validate-worker-response","update-progress","check-antipattern","error-flag-pattern","signature-scan","signature-match","flag-add","flag-check-blockers","flag-resolve","flag-acknowledge","flag-list","flag-auto-resolve","autofix-checkpoint","autofix-rollback","spawn-can-spawn-swarm","swarm-findings-init","swarm-findings-add","swarm-findings-read","swarm-solution-set","swarm-cleanup","swarm-activity-log","swarm-display-init","swarm-display-update","swarm-display-get","swarm-display-text","swarm-timing-start","swarm-timing-get","swarm-timing-eta","view-state-init","view-state-get","view-state-set","view-state-toggle","view-state-expand","view-state-collapse","grave-add","grave-check","phase-insert","generate-commit-message","version-check","registry-add","registry-list","bootstrap-system","chamber-create","chamber-verify","chamber-list","milestone-detect","queen-init","queen-read","queen-promote","incident-rule-add","survey-load","survey-verify","pheromone-export","pheromone-write","pheromone-count","pheromone-read","instinct-read","instinct-create","instinct-apply","pheromone-prime","colony-prime","pheromone-expire","eternal-init","eternal-store","pheromone-export-xml","pheromone-import-xml","pheromone-validate-xml","wisdom-export-xml","wisdom-import-xml","registry-export-xml","registry-import-xml","memory-metrics","midden-recent-failures","midden-review","midden-acknowledge","entropy-score","force-unlock","changelog-append","changelog-collect-plan-data","suggest-approve","suggest-quick-dismiss","data-clean","autopilot-init","autopilot-update","autopilot-status","autopilot-stop","autopilot-check-replan","hive-init","hive-store","hive-read","hive-abstract","hive-promote","init-research","charter-write","colony-name","emoji-audit"],
+  "commands": ["help","version","validate-state","validate-oracle-state","load-state","unload-state","error-add","error-pattern-check","error-summary","activity-log","activity-log-init","activity-log-read","learning-promote","learning-inject","learning-observe","learning-check-promotion","learning-promote-auto","memory-capture","queen-thresholds","context-capsule","rolling-summary","generate-ant-name","spawn-log","spawn-complete","spawn-can-spawn","spawn-get-depth","spawn-tree-load","spawn-tree-active","spawn-tree-depth","spawn-efficiency","validate-worker-response","update-progress","check-antipattern","error-flag-pattern","signature-scan","signature-match","flag-add","flag-check-blockers","flag-resolve","flag-acknowledge","flag-list","flag-auto-resolve","autofix-checkpoint","autofix-rollback","spawn-can-spawn-swarm","swarm-findings-init","swarm-findings-add","swarm-findings-read","swarm-solution-set","swarm-cleanup","swarm-activity-log","swarm-display-init","swarm-display-update","swarm-display-get","swarm-display-text","swarm-timing-start","swarm-timing-get","swarm-timing-eta","view-state-init","view-state-get","view-state-set","view-state-toggle","view-state-expand","view-state-collapse","grave-add","grave-check","phase-insert","generate-commit-message","version-check","registry-add","registry-list","bootstrap-system","chamber-create","chamber-verify","chamber-list","milestone-detect","queen-init","queen-read","queen-promote","incident-rule-add","survey-load","survey-verify","pheromone-export","pheromone-write","pheromone-count","pheromone-read","instinct-read","instinct-create","instinct-apply","pheromone-prime","colony-prime","pheromone-expire","eternal-init","eternal-store","pheromone-export-xml","pheromone-import-xml","pheromone-validate-xml","wisdom-export-xml","wisdom-import-xml","registry-export-xml","registry-import-xml","memory-metrics","midden-recent-failures","midden-review","midden-acknowledge","midden-search","midden-tag","entropy-score","force-unlock","changelog-append","changelog-collect-plan-data","suggest-approve","suggest-quick-dismiss","data-clean","autopilot-init","autopilot-update","autopilot-status","autopilot-stop","autopilot-check-replan","autopilot-set-headless","autopilot-headless-check","pending-decision-add","pending-decision-list","pending-decision-resolve","hive-init","hive-store","hive-read","hive-abstract","hive-promote","init-research","charter-write","colony-name","colony-vital-signs","emoji-audit","trophallaxis-diagnose","trophallaxis-retry","scar-add","scar-list","scar-check","immune-auto-scar","council-deliberate","council-advocate","council-challenger","council-sage","council-history","council-budget-check"],
   "sections": {
     "Core": [
       {"name": "help", "description": "List all available commands with sections"},
@@ -1250,6 +1254,7 @@ case "$cmd" in
       {"name": "pheromone-count", "description": "Count active pheromone signals"},
       {"name": "pheromone-prime", "description": "Prime the pheromone system"},
       {"name": "colony-prime", "description": "Assemble unified worker priming payload"},
+      {"name": "pr-context", "description": "Generate CI-ready colony context as structured JSON"},
       {"name": "pheromone-expire", "description": "Expire old pheromone signals"},
       {"name": "eternal-store", "description": "Store high-value signals in eternal memory"},
       {"name": "pheromone-export", "description": "Export pheromone data to JSON"},
@@ -1271,7 +1276,14 @@ case "$cmd" in
       {"name": "midden-recent-failures", "description": "Read recent failure signals from midden"},
       {"name": "midden-review", "description": "Review unacknowledged midden entries grouped by category"},
       {"name": "midden-acknowledge", "description": "Acknowledge midden entries by id or category"},
+      {"name": "midden-search", "description": "Search midden entries by keyword with optional category/source filters"},
+      {"name": "midden-tag", "description": "Add or remove a tag from a midden entry"},
+      {"name": "midden-collect", "description": "Collect failure records from a merged branch worktree into main midden"},
+      {"name": "midden-handle-revert", "description": "Tag entries from a reverted merge commit (preserves audit trail)"},
+      {"name": "midden-cross-pr-analysis", "description": "Detect failure patterns across multiple merged branches with auto-REDIRECT"},
+      {"name": "midden-prune", "description": "Prune stale merge records and acknowledge old reverted entries"},
       {"name": "entropy-score", "description": "Compute colony entropy score (0-100)"},
+      {"name": "colony-vital-signs", "description": "Compute colony health metrics from existing data (velocity, errors, signals, memory, overall score)"},
       {"name": "force-unlock", "description": "Emergency unlock — remove stale lock files"}
     ],
     "Changelog": [
@@ -1290,7 +1302,12 @@ case "$cmd" in
       {"name": "autopilot-update", "description": "Update autopilot state after phase action"},
       {"name": "autopilot-status", "description": "Return current autopilot state"},
       {"name": "autopilot-stop", "description": "Stop or complete an autopilot run with reason"},
-      {"name": "autopilot-check-replan", "description": "Check if replan trigger should fire based on completed phases"}
+      {"name": "autopilot-check-replan", "description": "Check if replan trigger should fire based on completed phases"},
+      {"name": "autopilot-set-headless", "description": "Set headless mode flag in run-state.json (true or false)"},
+      {"name": "autopilot-headless-check", "description": "Check if autopilot is running in headless mode"},
+      {"name": "pending-decision-add", "description": "Queue a deferred decision for later review"},
+      {"name": "pending-decision-list", "description": "List pending decisions, optionally filtered by type or status"},
+      {"name": "pending-decision-resolve", "description": "Mark a pending decision as resolved with a resolution note"}
     ],
     "Hive Intelligence": [
       {"name": "hive-init", "description": "Initialize ~/.aether/hive/ directory and wisdom.json schema"},
@@ -1318,6 +1335,28 @@ case "$cmd" in
     "Emoji Audit": [
       {"name": "emoji-audit", "description": "Audit emoji usage in command files against the canonical colony-visuals reference map"}
     ],
+    "Immune System": [
+      {"name": "trophallaxis-diagnose", "description": "Diagnose a task failure by searching midden for related failures and suggesting an approach"},
+      {"name": "trophallaxis-retry", "description": "Record a retry attempt for a task with diagnosis context injected"},
+      {"name": "scar-add", "description": "Record a persistent failure pattern as a scar to warn future workers"},
+      {"name": "scar-list", "description": "List scars, optionally filtered by active status or severity"},
+      {"name": "scar-check", "description": "Check if a task description matches any active scar patterns"},
+      {"name": "immune-auto-scar", "description": "Auto-create a scar if a task has been retried 3 or more times"}
+    ],
+    "Council": [
+      {"name": "council-deliberate", "description": "Start a new deliberation with Advocate/Challenger/Sage model and spawn budget guard"},
+      {"name": "council-advocate", "description": "Record an advocate argument (FOR) for a deliberation"},
+      {"name": "council-challenger", "description": "Record a challenger argument (AGAINST) for a deliberation"},
+      {"name": "council-sage", "description": "Record sage synthesis and recommendation, marks deliberation complete"},
+      {"name": "council-history", "description": "List past deliberations with their outcomes"},
+      {"name": "council-budget-check", "description": "Check if current spawn budget allows N more spawns"}
+    ],
+    "Clash Detection": [
+      {"name": "clash-check", "description": "Check if a file has conflicts across active worktrees"},
+      {"name": "clash-setup", "description": "Install or uninstall the PreToolUse clash detection hook"},
+      {"name": "worktree-create", "description": "Create a git worktree with colony context copy"},
+      {"name": "worktree-cleanup", "description": "Remove a git worktree and clean up tracking"}
+    ],
     "Deprecated": [
       {"name": "checkpoint-check", "description": "Check dirty files against allowlist [DEPRECATED]"},
       {"name": "error-pattern-check", "description": "Check for error anti-patterns [DEPRECATED]"},
@@ -1348,7 +1387,7 @@ HELP_EOF
     _pkg_json="$SCRIPT_DIR/../package.json"
     if [[ -f "$_pkg_json" ]] && command -v jq >/dev/null 2>&1; then  # SUPPRESS:OK -- cleanup: output suppression for clean operation
       _ver=$(jq -r '.version // "unknown"' "$_pkg_json" 2>/dev/null)  # SUPPRESS:OK -- read-default: file may not exist yet
-      json_ok "\"$_ver\""
+      json_ok "$(jq -nc --arg v "$_ver" '$v')"
     else
       json_ok '"1.1.5"'
     fi
@@ -1381,6 +1420,7 @@ HELP_EOF
         ;;
       constraints)
         [[ -f "$COLONY_DATA_DIR/constraints.json" ]] || json_err "$E_FILE_NOT_FOUND" "constraints.json not found" '{"file":"constraints.json"}'
+        [[ -s "$COLONY_DATA_DIR/constraints.json" ]] || { json_ok '{"file":"constraints.json","checks":["pass","pass"],"pass":true}'; exit 0; }
         json_ok "$(jq '
           def arr(f): if has(f) and (.[f]|type) == "array" then "pass" else "fail: \(f) not array" end;
           {file:"constraints.json", checks:[
@@ -1428,7 +1468,7 @@ HELP_EOF
       json_err "$E_FEATURE_UNAVAILABLE" "create_backup function not available -- atomic-write.sh may not be sourced"
     fi
 
-    json_ok "{\"checkpointed\":true,\"reason\":\"$sc_reason\"}"
+    json_ok "$(jq -nc --arg reason "$sc_reason" '{checkpointed:true,reason:$reason}')"
     ;;
   state-write)
     # MIGRATE: direct COLONY_STATE.json access -- use _state_write instead
@@ -1670,7 +1710,7 @@ HELP_EOF
         if (.errors.records|length) > 50 then .errors.records = .errors.records[-50:] else . end
       ' >/dev/null
 
-    json_ok "\"$ea_id\""
+    json_ok "$(jq -nc --arg id "$ea_id" '$id')"
     ;;
   error-pattern-check)
     _deprecation_warning "error-pattern-check"
@@ -1707,6 +1747,12 @@ HELP_EOF
       exit 0
     fi
 
+    # Skip writes during test runs to prevent test noise in activity.log
+    if [[ "${AETHER_TESTING:-}" == "1" ]]; then
+      json_ok '"logged"'
+      exit 0
+    fi
+
     log_file="$COLONY_DATA_DIR/activity.log"
     mkdir -p "$COLONY_DATA_DIR"
     ts=$(date -u +"%H:%M:%S")
@@ -1857,7 +1903,7 @@ EOF
         json_err "$E_UNKNOWN" "Failed to write error patterns file"
       }
       count=$(echo "$updated" | jq --arg name "$pattern_name" '.patterns[] | select(.name == $name) | .occurrences')
-      json_ok "{\"updated\":true,\"pattern\":\"$pattern_name\",\"occurrences\":$count}"
+      json_ok "$(jq -nc --arg p "$pattern_name" --argjson c "$count" '{updated:true,pattern:$p,occurrences:$c}')"
     else
       # Add new pattern
       updated=$(jq --arg name "$pattern_name" --arg desc "$description" --arg sev "$severity" --arg ts "$ts" --arg proj "$project_name" '
@@ -1876,7 +1922,7 @@ EOF
         _aether_log_error "Could not save new error pattern"
         json_err "$E_UNKNOWN" "Failed to write error patterns file"
       }
-      json_ok "{\"created\":true,\"pattern\":\"$pattern_name\"}"
+      json_ok "$(jq -nc --arg p "$pattern_name" '{created:true,pattern:$p}')"
     fi
     ;;
   error-patterns-check)
@@ -2159,7 +2205,7 @@ EOF
     prefix="${prefixes[$idx]}"
     num=$((RANDOM % 99 + 1))
     name="${prefix}-${num}"
-    json_ok "\"$name\""
+    json_ok "$(jq -nc --arg n "$name" '$n')"
     ;;
 
   validate-worker-response)
@@ -2260,7 +2306,7 @@ EOF
       json_err "$E_VALIDATION_FAILED" "Worker response failed schema validation" "{\"caste\":\"$vw_caste\"}"
     fi
 
-    json_ok "{\"valid\":true,\"caste\":\"$vw_caste\"}"
+    json_ok "$(jq -nc --arg c "$vw_caste" '{valid:true,caste:$c}')"
     ;;
 
   # ============================================
@@ -2315,7 +2361,7 @@ EOF
         if (.graveyards | length) > 30 then .graveyards = .graveyards[-30:] else . end
       ' >/dev/null
 
-    json_ok "\"$ga_id\""
+    json_ok "$(jq -nc --arg id "$ga_id" '$id')"
     ;;
 
   grave-check)
@@ -2414,7 +2460,7 @@ Files: ${files_changed} files changed"
         fi
 
         # Return enhanced JSON with additional metadata
-        json_ok "{\"message\":\"$message\",\"body\":\"$body\",\"files_changed\":$files_changed,\"subsystem\":\"$subsystem\",\"scope\":\"${phase_id}.${plan_num}\"}"
+        json_ok "$(jq -nc --arg msg "$message" --arg body "$body" --arg sub "$subsystem" --arg scope "${phase_id}.${plan_num}" '{message:$msg,body:$body,files_changed:'"$files_changed"',subsystem:$sub,scope:$scope}')"
         exit 0
         ;;
       seal)
@@ -2436,7 +2482,7 @@ Files: ${files_changed} files changed"
           message="${message:0:69}..."
         fi
 
-        json_ok "{\"message\":\"$message\",\"body\":\"$body\",\"files_changed\":$files_changed}"
+        json_ok "$(jq -nc --arg msg "$message" --arg body "$body" '{message:$msg,body:$body,files_changed:'"$files_changed"'}')"
         exit 0
         ;;
       *)
@@ -2450,7 +2496,7 @@ Files: ${files_changed} files changed"
       message="${message:0:69}..."
     fi
 
-    json_ok "{\"message\":\"$message\",\"body\":\"$body\",\"files_changed\":$files_changed}"
+    json_ok "$(jq -nc --arg msg "$message" --arg body "$body" '{message:$msg,body:$body,files_changed:'"$files_changed"'}')"
     ;;
 
   # ============================================
@@ -2502,7 +2548,7 @@ Files: ${files_changed} files changed"
       json_ok '""'
     else
       printf -v msg 'Update available: %s to %s (run /ant:update)' "$local_ver" "$hub_ver"
-      json_ok "$msg"
+      json_ok "$(jq -nc --arg m "$msg" '$m')"
     fi
     ;;
 
@@ -2628,7 +2674,7 @@ Files: ${files_changed} files changed"
       json_err "$E_UNKNOWN" "Failed to write registry file"
     }
     release_lock "$registry_file" 2>/dev/null || true  # SUPPRESS:OK -- cleanup: lock may not be held
-    json_ok "{\"registered\":true,\"path\":\"$repo_path\",\"version\":\"$repo_version\"}"
+    json_ok "$(jq -nc --arg p "$repo_path" --arg v "$repo_version" '{registered:true,path:$p,version:$v}')"
     ;;
 
   registry-list)
@@ -2773,7 +2819,8 @@ Files: ${files_changed} files changed"
     if [[ $? -eq 0 ]]; then
       # Output success with handoff info if detected
       if [[ "$HANDOFF_DETECTED" == "true" ]]; then
-        json_ok "{\"loaded\":true,\"handoff_detected\":true,\"handoff_summary\":\"$(get_handoff_summary)\"}"
+        _handoff_summary=$(get_handoff_summary)
+        json_ok "$(jq -nc --arg hs "$_handoff_summary" '{loaded:true,handoff_detected:true,handoff_summary:$hs}')"
       else
         json_ok '{"loaded":true}'
       fi
@@ -3110,10 +3157,10 @@ Files: ${files_changed} files changed"
       json_ok "$(cat "$view_state_file")"
     elif [[ -z "$key" ]]; then
       # Return specific view
-      json_ok "$(jq ".${view_name} // {}" "$view_state_file")"
+      json_ok "$(jq --arg v "$view_name" '.[$v] // {}' "$view_state_file")"
     else
       # Return specific key from view
-      json_ok "$(jq ".${view_name}.${key} // null" "$view_state_file")"
+      json_ok "$(jq --arg v "$view_name" --arg k "$key" '.[$v][$k] // null' "$view_state_file")"
     fi
     ;;
 
@@ -3145,7 +3192,7 @@ Files: ${files_changed} files changed"
     fi
 
     atomic_write "$view_state_file" "$updated"
-    json_ok "$(echo "$updated" | jq ".${view_name}")"
+    json_ok "$(echo "$updated" | jq --arg v "$view_name" '.[$v]')"
     ;;
 
   view-state-toggle)
@@ -3183,7 +3230,7 @@ Files: ${files_changed} files changed"
     fi
 
     atomic_write "$view_state_file" "$updated"
-    json_ok "{\"item\":\"$item\",\"state\":\"$new_state\",\"view\":\"$view_name\"}"
+    json_ok "$(jq -nc --arg i "$item" --arg s "$new_state" --arg v "$view_name" '{item:$i,state:$s,view:$v}')"
     ;;
 
   view-state-expand)
@@ -3205,7 +3252,7 @@ Files: ${files_changed} files changed"
     ' "$view_state_file") || json_err "$E_JSON_INVALID" "Failed to update view state"
 
     atomic_write "$view_state_file" "$updated"
-    json_ok "{\"item\":\"$item\",\"state\":\"expanded\",\"view\":\"$view_name\"}"
+    json_ok "$(jq -nc --arg i "$item" --arg v "$view_name" '{item:$i,state:"expanded",view:$v}')"
     ;;
 
   view-state-collapse)
@@ -3227,7 +3274,7 @@ Files: ${files_changed} files changed"
     ' "$view_state_file") || json_err "$E_JSON_INVALID" "Failed to update view state"
 
     atomic_write "$view_state_file" "$updated"
-    json_ok "{\"item\":\"$item\",\"state\":\"collapsed\",\"view\":\"$view_name\"}"
+    json_ok "$(jq -nc --arg i "$item" --arg v "$view_name" '{item:$i,state:"collapsed",view:$v}')"
     ;;
 
   queen-init) _queen_init "$@" ;;
@@ -3294,7 +3341,7 @@ Files: ${files_changed} files changed"
       bar="[$bar]"
     fi
 
-    json_ok "{\"bar\":\"$bar\",\"count\":$obs_count,\"threshold\":$threshold}"
+    json_ok "$(jq -nc --arg b "$bar" --argjson c "$obs_count" --argjson t "$threshold" '{bar:$b,count:$c,threshold:$t}')"
     ;;
 
   parse-selection)
@@ -3501,7 +3548,7 @@ Files: ${files_changed} files changed"
         ;;
     esac
 
-    json_ok "{\"incident_id\":\"$ir_incident_id\",\"rule_type\":\"$ir_rule_type\",\"added\":true,\"timestamp\":\"$ir_ts\"}"
+    json_ok "$(jq -nc --arg id "$ir_incident_id" --arg rt "$ir_rule_type" --arg ts "$ir_ts" '{incident_id:$id,rule_type:$rt,added:true,timestamp:$ts}')"
     ;;
 
   queen-promote) _queen_promote "$@" ;;
@@ -3630,7 +3677,7 @@ Files: ${files_changed} files changed"
     bash "$0" rolling-summary add "$mc_event" "$mc_content" "$mc_source" >/dev/null 2>&1 \
       || _aether_log_error "Could not update rolling summary"
 
-    json_ok "{\"event_type\":\"$mc_event\",\"wisdom_type\":\"$mc_wisdom_type\",\"observation_count\":$obs_count,\"threshold\":$obs_threshold,\"threshold_met\":$obs_threshold_met,\"pheromone_created\":$pheromone_created,\"signal_id\":\"$pheromone_signal_id\",\"auto_promoted\":$auto_promoted,\"promotion_reason\":\"$auto_reason\"}"
+    json_ok "$(jq -nc --arg et "$mc_event" --arg wt "$mc_wisdom_type" --argjson oc "$obs_count" --argjson th "$obs_threshold" --argjson tm "$obs_threshold_met" --argjson pc "$pheromone_created" --arg sid "$pheromone_signal_id" --argjson ap "$auto_promoted" --arg pr "$auto_reason" '{event_type:$et,wisdom_type:$wt,observation_count:$oc,threshold:$th,threshold_met:$tm,pheromone_created:$pc,signal_id:$sid,auto_promoted:$ap,promotion_reason:$pr}')"
     ;;
 
   learning-display-proposals) _learning_display_proposals "$@" ;;
@@ -3675,7 +3722,7 @@ Files: ${files_changed} files changed"
         ;;
     esac
 
-    json_ok "{\"ok\":true,\"docs\":\"$docs\",\"dir\":\"$survey_dir\"}"
+    json_ok "$(jq -nc --arg d "$docs" --arg dir "$survey_dir" '{ok:true,docs:$d,dir:$dir}')"
     ;;
 
   survey-verify)
@@ -3697,7 +3744,7 @@ Files: ${files_changed} files changed"
       json_err "$E_FILE_NOT_FOUND" "Missing survey documents" "{\"missing\":\"$missing\"}"
     fi
 
-    json_ok "{\"ok\":true,\"counts\":\"$counts\"}"
+    json_ok "$(jq -nc --arg c "$counts" '{ok:true,counts:$c}')"
     ;;
 
   checkpoint-check)
@@ -3869,6 +3916,7 @@ Files: ${files_changed} files changed"
 
   pheromone-prime) _pheromone_prime "$@" ;;
   colony-prime) _colony_prime "$@" ;;
+  pr-context) _pr_context "$@" ;;
   pheromone-expire) _pheromone_expire "$@" ;;
   eternal-init) _eternal_init "$@" ;;
   eternal-store) _eternal_store "$@" ;;
@@ -4101,7 +4149,7 @@ Files: ${files_changed} files changed"
           json_err "$E_UNKNOWN" "Failed to finalize rolling summary file"
         }
 
-        json_ok "{\"added\":true,\"event\":\"$rs_clean_event\",\"source\":\"$rs_clean_source\"}"
+        json_ok "$(jq -nc --arg e "$rs_clean_event" --arg s "$rs_clean_source" '{added:true,event:$e,source:$s}')"
         ;;
 
       read)
@@ -4330,7 +4378,7 @@ Files: ${files_changed} files changed"
 
     cc_words=$(printf '%s' "$cc_section" | wc -w | tr -d ' ')
     cc_prompt_json=$(printf '%s' "$cc_section" | jq -Rs '.' 2>/dev/null || echo '""')  # SUPPRESS:OK -- read-default: returns fallback if missing
-    json_ok "{\"exists\":true,\"state\":\"$cc_state\",\"next_action\":\"$cc_next_action\",\"word_count\":$cc_words,\"prompt_section\":$cc_prompt_json}"
+    json_ok "$(jq -nc --arg st "$cc_state" --arg na "$cc_next_action" --argjson wc "$cc_words" --argjson ps "$cc_prompt_json" '{exists:true,state:$st,next_action:$na,word_count:$wc,prompt_section:$ps}')"
     ;;
 
   session-init) _session_init "$@" ;;
@@ -4341,6 +4389,13 @@ Files: ${files_changed} files changed"
   session-mark-resumed) _session_mark_resumed "$@" ;;
   session-summary) _session_summary "$@" ;;
 
+  pending-decision-add) _pending_decision_add "$@" ;;
+  pending-decision-list) _pending_decision_list "$@" ;;
+  pending-decision-resolve) _pending_decision_resolve "$@" ;;
+
+  autopilot-headless-check) _autopilot_headless_check "$@" ;;
+  autopilot-set-headless) _autopilot_set_headless "$@" ;;
+
   generate-progress-bar)
     generate-progress-bar "$@"
     ;;
@@ -4717,6 +4772,40 @@ EOF
 
   midden-acknowledge) _midden_acknowledge "$@" ;;
 
+  midden-search) _midden_search "$@" ;;
+
+  midden-tag) _midden_tag "$@" ;;
+
+  midden-collect) _midden_collect "$@" ;;
+  midden-handle-revert) _midden_handle_revert "$@" ;;
+  midden-cross-pr-analysis) _midden_cross_pr_analysis "$@" ;;
+  midden-prune) _midden_prune "$@" ;;
+
+  trophallaxis-diagnose) _trophallaxis_diagnose "$@" ;;
+
+  trophallaxis-retry) _trophallaxis_retry "$@" ;;
+
+  scar-add) _scar_add "$@" ;;
+
+  scar-list) _scar_list "$@" ;;
+
+  scar-check) _scar_check "$@" ;;
+
+  immune-auto-scar) _immune_auto_scar "$@" ;;
+
+  # ── Council Deliberation ────────────────────────────────────────────────────
+  council-deliberate) _council_deliberate "$@" ;;
+
+  council-advocate) _council_advocate "$@" ;;
+
+  council-challenger) _council_challenger "$@" ;;
+
+  council-sage) _council_sage "$@" ;;
+
+  council-history) _council_history "$@" ;;
+
+  council-budget-check) _council_budget_check "$@" ;;
+
   resume-dashboard)
     # Generate dashboard data for /ant:resume command
     # Usage: resume-dashboard
@@ -4798,6 +4887,14 @@ EOF
     exit 0
     ;;
 
+  colony-vital-signs)
+    # Compute colony health metrics from existing data files
+    # Usage: colony-vital-signs
+    # Returns: JSON with build_velocity, error_rate, signal_health, memory_pressure,
+    #          colony_age_hours, and overall_health (0-100)
+    _colony_vital_signs
+    ;;
+
   data-safety-stats)
     # Read data safety statistics from safety-stats.json
     # Usage: data-safety-stats
@@ -4820,6 +4917,8 @@ EOF
     exit 0
     ;;
 
+  # colony-vital-signs handled above (dispatches to _colony_vital_signs in state-api.sh)
+
   suggest-analyze) _suggest_analyze "$@" ;;
   suggest-record) _suggest_record "$@" ;;
   suggest-check) _suggest_check "$@" ;;
@@ -5348,6 +5447,22 @@ DRYRUN_EOF
     _emoji_audit_main "${1:-$(pwd)}"
     ;;
 
+  # ── Clash Detection ─────────────────────────────────────────────────────────
+  clash-detect|clash-check)
+    _clash_detect "$@"
+    ;;
+  clash-setup)
+    _clash_setup "$@"
+    ;;
+
+  # ── Worktree Management ─────────────────────────────────────────────────────
+  worktree-create)
+    _worktree_create "$@"
+    ;;
+  worktree-cleanup)
+    _worktree_cleanup "$@"
+    ;;
+
   *)
     json_err "$E_VALIDATION_FAILED" "Unknown command: $cmd"
     ;;