aether-colony 5.3.2 → 5.4.0

package/.aether/commands/seal.yaml

@@ -57,7 +57,7 @@ body_claude: |
 
   ### Step 2: Maturity Gate
 
-  Run `bash .aether/aether-utils.sh milestone-detect` to get `milestone`, `phases_completed`, `total_phases`.
+  Run `aether milestone-detect` to get `milestone`, `phases_completed`, `total_phases`.
 
   **If milestone is already "Crowned Anthill":**
   ```
@@ -119,8 +119,8 @@ body_claude: |
 
   if [[ "$phases_completed" -ge 3 ]]; then
     # Generate Sage name and dispatch
-    sage_name=$(bash .aether/aether-utils.sh generate-ant-name "sage")
-    bash .aether/aether-utils.sh spawn-log "Queen" "sage" "$sage_name" "Colony analytics review"
+    sage_name=$(aether generate-ant-name --caste "sage")
+    aether spawn-log --name "Queen" --caste "sage" --id "$sage_name" --description "Colony analytics review"
 
     # Display spawn notification
     echo ""
@@ -159,7 +159,7 @@ body_claude: |
 
   **IMPORTANT:** You are strictly read-only. Do not modify any files.
 
-  Log activity: bash .aether/aether-utils.sh activity-log "ANALYZING" "{sage_name}" "description"
+  Log activity: aether activity-log "ANALYZING" "{sage_name}" "description"
 
   Return ONLY this JSON (no other text):
   {{
@@ -192,7 +192,7 @@ body_claude: |
 
   Log completion and update swarm display:
   ```bash
-  bash .aether/aether-utils.sh spawn-complete "$sage_name" "completed" "Analytics review complete"
+  aether spawn-complete --id "$sage_name" --status "completed" --summary "Analytics review complete"
   ```
 
   **Display Sage completion line:**
@@ -204,7 +204,7 @@ body_claude: |
   **Log high-priority recommendations to midden (non-blocking):**
   For each recommendation with priority <= 2:
   ```bash
-  bash .aether/aether-utils.sh midden-write "analytics" "Sage recommendation (P{priority}): {action}" "sage"
+  aether midden-write "analytics" "Sage recommendation (P{priority}): {action}" "sage"
   ```
 
   **Display insights summary:**
@@ -239,7 +239,7 @@ body_claude: |
       colony=$(echo "$encoded" | base64 -d | jq -r '.colonies[0] // "unknown"')
       [[ -z "$content" ]] && continue
 
-      result=$(bash .aether/aether-utils.sh learning-promote-auto "$wisdom_type" "$content" "$colony" "learning" 2>/dev/null || echo '{}')
+      result=$(aether learning-promote-auto "$wisdom_type" "$content" "$colony" "learning" 2>/dev/null || echo '{}')
       was_promoted=$(echo "$result" | jq -r '.result.promoted // false' 2>/dev/null || echo "false")
       if [[ "$was_promoted" == "true" ]]; then
         auto_promoted_count=$((auto_promoted_count + 1))
@@ -254,7 +254,7 @@ body_claude: |
   # --- END Batch auto-promotion ---
 
   # Check for pending proposals
-  proposals=$(bash .aether/aether-utils.sh learning-check-promotion 2>/dev/null || echo '{"proposals":[]}')
+  proposals=$(aether learning-check-promotion 2>/dev/null || echo '{"proposals":[]}')
   proposal_count=$(echo "$proposals" | jq '.proposals | length')
 
   if [[ "$proposal_count" -gt 0 ]]; then
@@ -268,7 +268,7 @@ body_claude: |
     echo ""
 
     # Run approval workflow (blocking)
-    bash .aether/aether-utils.sh learning-approve-proposals
+    aether learning-approve-proposals
 
     echo ""
     echo "Wisdom review complete. Proceeding with sealing ceremony..."
@@ -318,7 +318,7 @@ body_claude: |
     [[ -n "$repo_domain_tags" ]] && promote_args+=(--domain "$repo_domain_tags")
 
     # Call hive-promote which orchestrates abstract + store
-    result=$(bash .aether/aether-utils.sh "${promote_args[@]}" 2>/dev/null || echo '{}')
+    result=$(aether "${promote_args[@]}" 2>/dev/null || echo '{}')
     was_promoted=$(echo "$result" | jq -r '.result.action // "skipped"' 2>/dev/null || echo "skipped")
 
     if [[ "$was_promoted" == "promoted" || "$was_promoted" == "merged" ]]; then
@@ -338,7 +338,7 @@ body_claude: |
 
   Log the seal ceremony to activity log:
   ```bash
-  bash .aether/aether-utils.sh activity-log "MODIFIED" "Queen" "Colony sealed - wisdom review completed"
+  aether activity-log "MODIFIED" "Queen" "Colony sealed - wisdom review completed"
   ```
 
   ### Step 4.4: Checkpoint State
@@ -347,7 +347,7 @@ body_claude: |
 
   Run using the Bash tool with description "Checkpointing colony state before seal...":
   ```bash
-  bash .aether/aether-utils.sh state-checkpoint "pre-seal" 2>/dev/null || echo "Warning: State checkpoint failed -- continuing without backup" >&2
+  aether state-checkpoint "pre-seal" 2>/dev/null || echo "Warning: State checkpoint failed -- continuing without backup" >&2
   ```
 
   ### Step 4.5: Increment Colony Version
@@ -382,7 +382,7 @@ body_claude: |
   2. Set `milestone_updated_at` to current ISO-8601 timestamp
   3. Append event: `"<timestamp>|milestone_reached|seal|Achieved Crowned Anthill milestone"`
 
-  Run `bash .aether/aether-utils.sh validate-state colony` after write.
+  Run `aether validate-state colony` after write.
 
   ### Step 5.1: Update Changelog
 
@@ -395,7 +395,7 @@ body_claude: |
   - Summarize the goal and key outcomes in one line
 
   ```bash
-  bash .aether/aether-utils.sh changelog-append \
+  aether changelog-append \
     "$(date +%Y-%m-%d)" \
     "seal-crowned-anthill" \
     "00" \
@@ -416,7 +416,7 @@ body_claude: |
 
   Run using the Bash tool (ignore errors):
   ```bash
-  bash .aether/aether-utils.sh registry-add "$(pwd)" "$(jq -r '.version // "unknown"' ~/.aether/version.json 2>/dev/null || echo 'unknown')" --active false 2>/dev/null || true
+  aether registry-add --path "$(pwd)" "$(jq -r '.version // "unknown"' ~/.aether/version.json 2>/dev/null || echo 'unknown')" --active false 2>/dev/null || true
   ```
 
   If the command fails, proceed silently. This is optional bookkeeping.
@@ -428,10 +428,10 @@ body_claude: |
   **Generate Chronicler name and dispatch:**
   ```bash
   # Generate unique chronicler name
-  chronicler_name=$(bash .aether/aether-utils.sh generate-ant-name "chronicler")
+  chronicler_name=$(aether generate-ant-name --caste "chronicler")
 
   # Log spawn and update swarm display
-  bash .aether/aether-utils.sh spawn-log "Queen" "chronicler" "$chronicler_name" "Documentation coverage audit"
+  aether spawn-log --name "Queen" --caste "chronicler" --id "$chronicler_name" --description "Documentation coverage audit"
   ```
 
   **Display:**
@@ -469,7 +469,7 @@ body_claude: |
 
   **IMPORTANT:** You are strictly read-only. Do not modify any files.
 
-  Log activity: bash .aether/aether-utils.sh activity-log "SURVEYING" "{chronicler_name}" "description"
+  Log activity: aether activity-log "SURVEYING" "{chronicler_name}" "description"
 
   Return ONLY this JSON (no other text):
   {
@@ -498,7 +498,7 @@ body_claude: |
 
   Log completion and update swarm display:
   ```bash
-  bash .aether/aether-utils.sh spawn-complete "$chronicler_name" "completed" "Documentation audit complete"
+  aether spawn-complete --id "$chronicler_name" --status "completed" --summary "Documentation audit complete"
   ```
 
   **Display Chronicler completion line:**
@@ -509,7 +509,7 @@ body_claude: |
   **Log gaps to midden (non-blocking):**
   For each gap in `gaps_identified` with severity "high" or "medium":
   ```bash
-  bash .aether/aether-utils.sh midden-write "documentation" "Gap ({severity}): {description} at {location}" "chronicler"
+  aether midden-write "documentation" "Gap ({severity}): {description} at {location}" "chronicler"
   ```
 
   **Display summary:**
@@ -580,7 +580,7 @@ body_claude: |
   ```bash
   # Check if xmllint is available
   if command -v xmllint >/dev/null 2>&1; then
-    xml_result=$(bash .aether/aether-utils.sh colony-archive-xml ".aether/exchange/colony-archive.xml" 2>&1)
+    xml_result=$(aether colony-archive-xml --output ".aether/exchange/colony-archive.xml" 2>&1)
     xml_ok=$(echo "$xml_result" | jq -r '.ok // false' 2>/dev/null)
     if [[ "$xml_ok" == "true" ]]; then
       xml_pheromone_count=$(echo "$xml_result" | jq -r '.result.pheromone_count // 0' 2>/dev/null)
@@ -590,7 +590,7 @@ body_claude: |
     fi
 
     # Also export standalone pheromones.xml for cross-colony sharing
-    pher_result=$(bash .aether/aether-utils.sh pheromone-export-xml ".aether/exchange/pheromones.xml" 2>&1)
+    pher_result=$(aether pheromone-export-xml --output ".aether/exchange/pheromones.xml" 2>&1)
     pher_ok=$(echo "$pher_result" | jq -r '.ok // false' 2>/dev/null)
     if [[ "$pher_ok" == "true" ]]; then
       pher_signal_count=$(jq '[.signals[] | select(.active != false)] | length' .aether/data/pheromones.json 2>/dev/null || echo "0")
@@ -600,7 +600,7 @@ body_claude: |
     fi
 
     # Export standalone queen-wisdom.xml for cross-colony wisdom sharing
-    wisdom_result=$(bash .aether/aether-utils.sh wisdom-export-xml ".aether/exchange/queen-wisdom.xml" 2>&1)
+    wisdom_result=$(aether wisdom-export-xml ".aether/exchange/queen-wisdom.xml" 2>&1)
     wisdom_ok=$(echo "$wisdom_result" | jq -r '.ok // false' 2>/dev/null)
     if [[ "$wisdom_ok" == "true" ]]; then
       wisdom_count=$(echo "$wisdom_result" | jq -r '.result.entries // 0' 2>/dev/null)
@@ -610,7 +610,7 @@ body_claude: |
     fi
 
     # Export standalone colony-registry.xml for lineage tracking
-    registry_result=$(bash .aether/aether-utils.sh registry-export-xml ".aether/exchange/colony-registry.xml" 2>&1)
+    registry_result=$(aether registry-export-xml ".aether/exchange/colony-registry.xml" 2>&1)
     registry_ok=$(echo "$registry_result" | jq -r '.ok // false' 2>/dev/null)
     if [[ "$registry_ok" == "true" ]]; then
       registry_count=$(echo "$registry_result" | jq -r '.result.colonies // 0' 2>/dev/null)
@@ -689,7 +689,7 @@ body_claude: |
 
   Generate a seal commit message:
   ```bash
-  seal_commit=$(bash .aether/aether-utils.sh generate-commit-message seal "$phases_completed" "$goal" "$colony_age_days" 2>/dev/null)
+  seal_commit=$(aether generate-commit-message seal "$phases_completed" "$goal" "$colony_age_days" 2>/dev/null)
   seal_message=$(echo "$seal_commit" | jq -r '.result.message // "aether-seal: colony sealed"')
   seal_body=$(echo "$seal_commit" | jq -r '.result.body // ""')
   ```
@@ -932,7 +932,7 @@ body_opencode: |
   - Summarize the goal and key outcomes in one line
 
   ```bash
-  bash .aether/aether-utils.sh changelog-append \
+  aether changelog-append \
     "$(date +%Y-%m-%d)" \
     "seal-crowned-anthill" \
     "00" \
@@ -953,7 +953,7 @@ body_opencode: |
 
   Run using the Bash tool (ignore errors):
   ```bash
-  bash .aether/aether-utils.sh registry-add "$(pwd)" "$(jq -r '.version // "unknown"' ~/.aether/version.json 2>/dev/null || echo 'unknown')" --active false 2>/dev/null || true
+  aether registry-add --path "$(pwd)" "$(jq -r '.version // "unknown"' ~/.aether/version.json 2>/dev/null || echo 'unknown')" --active false 2>/dev/null || true
   ```
 
   If the command fails, proceed silently. This is optional bookkeeping.
@@ -998,7 +998,7 @@ body_opencode: |
     [[ -n "$repo_domain_tags" ]] && promote_args+=(--domain "$repo_domain_tags")
 
     # Call hive-promote which orchestrates abstract + store
-    result=$(bash .aether/aether-utils.sh "${promote_args[@]}" 2>/dev/null || echo '{}')
+    result=$(aether "${promote_args[@]}" 2>/dev/null || echo '{}')
     was_promoted=$(echo "$result" | jq -r '.result.action // "skipped"' 2>/dev/null || echo "skipped")
 
     if [[ "$was_promoted" == "promoted" || "$was_promoted" == "merged" ]]; then
@@ -1044,7 +1044,7 @@ body_opencode: |
   ```bash
   # Check if xmllint is available
   if command -v xmllint >/dev/null 2>&1; then
-    xml_result=$(bash .aether/aether-utils.sh colony-archive-xml ".aether/exchange/colony-archive.xml" 2>&1)
+    xml_result=$(aether colony-archive-xml --output ".aether/exchange/colony-archive.xml" 2>&1)
     xml_ok=$(echo "$xml_result" | jq -r '.ok // false' 2>/dev/null)
     if [[ "$xml_ok" == "true" ]]; then
       xml_pheromone_count=$(echo "$xml_result" | jq -r '.result.pheromone_count // 0' 2>/dev/null)
@@ -1054,7 +1054,7 @@ body_opencode: |
     fi
 
     # Also export standalone pheromones.xml for cross-colony sharing
-    pher_result=$(bash .aether/aether-utils.sh pheromone-export-xml ".aether/exchange/pheromones.xml" 2>&1)
+    pher_result=$(aether pheromone-export-xml --output ".aether/exchange/pheromones.xml" 2>&1)
     pher_ok=$(echo "$pher_result" | jq -r '.ok // false' 2>/dev/null)
     if [[ "$pher_ok" == "true" ]]; then
       pher_signal_count=$(jq '[.signals[] | select(.active != false)] | length' .aether/data/pheromones.json 2>/dev/null || echo "0")
@@ -1064,7 +1064,7 @@ body_opencode: |
     fi
 
     # Export standalone queen-wisdom.xml for cross-colony wisdom sharing
-    wisdom_result=$(bash .aether/aether-utils.sh wisdom-export-xml ".aether/exchange/queen-wisdom.xml" 2>&1)
+    wisdom_result=$(aether wisdom-export-xml ".aether/exchange/queen-wisdom.xml" 2>&1)
     wisdom_ok=$(echo "$wisdom_result" | jq -r '.ok // false' 2>/dev/null)
     if [[ "$wisdom_ok" == "true" ]]; then
       wisdom_count=$(echo "$wisdom_result" | jq -r '.result.entries // 0' 2>/dev/null)
@@ -1074,7 +1074,7 @@ body_opencode: |
     fi
 
     # Export standalone colony-registry.xml for lineage tracking
-    registry_result=$(bash .aether/aether-utils.sh registry-export-xml ".aether/exchange/colony-registry.xml" 2>&1)
+    registry_result=$(aether registry-export-xml ".aether/exchange/colony-registry.xml" 2>&1)
     registry_ok=$(echo "$registry_result" | jq -r '.ok // false' 2>/dev/null)
     if [[ "$registry_ok" == "true" ]]; then
       registry_count=$(echo "$registry_result" | jq -r '.result.colonies // 0' 2>/dev/null)
@@ -1145,7 +1145,7 @@ body_opencode: |
 
   Generate a seal commit message:
   ```bash
-  seal_commit=$(bash .aether/aether-utils.sh generate-commit-message seal "$phases_completed" "$goal" "$colony_age_days" 2>/dev/null)
+  seal_commit=$(aether generate-commit-message seal "$phases_completed" "$goal" "$colony_age_days" 2>/dev/null)
   seal_message=$(echo "$seal_commit" | jq -r '.result.message // "aether-seal: colony sealed"')
   seal_body=$(echo "$seal_commit" | jq -r '.result.body // ""')
   ```

package/.aether/commands/skill-create.yaml

@@ -225,7 +225,7 @@ body_claude: |
   Run using the Bash tool with description "Verifying skill frontmatter...":
 
   ```bash
-  bash .aether/aether-utils.sh skill-parse-frontmatter ~/.aether/skills/domain/{SKILL_NAME}/SKILL.md
+  aether skill-parse-frontmatter ~/.aether/skills/domain/{SKILL_NAME}/SKILL.md
   ```
 
   Check the output. If the result contains `"ok": true` (or the parsed JSON shows the correct name and type), the skill is valid. If parsing fails, fix the frontmatter and retry once.
@@ -235,7 +235,7 @@ body_claude: |
   Run using the Bash tool with description "Rebuilding skill cache...":
 
   ```bash
-  bash .aether/aether-utils.sh skill-cache-rebuild
+  aether skill-cache-rebuild
   ```
 
   **4d. Show the result**
@@ -330,8 +330,8 @@ body_opencode: |
   ### Step 4: Write and Verify
 
   1. Write to `~/.aether/skills/domain/{name}/SKILL.md`
-  2. Run: `bash .aether/aether-utils.sh skill-parse-frontmatter ~/.aether/skills/domain/{name}/SKILL.md`
-  3. Run: `bash .aether/aether-utils.sh skill-cache-rebuild`
+  2. Run: `aether skill-parse-frontmatter ~/.aether/skills/domain/{name}/SKILL.md`
+  3. Run: `aether skill-cache-rebuild`
   4. Show the generated skill to the user
   5. Ask if they want to adjust anything
 

package/.aether/commands/status.yaml

@@ -8,7 +8,7 @@ body: |
 
   ### Step 0: Version Check (Non-blocking)
 
-  {{TOOL_PREFIX "Checking colony version..."}} `bash .aether/aether-utils.sh version-check-cached 2>/dev/null || true`
+  {{TOOL_PREFIX "Checking colony version..."}} `aether version-check-cached 2>/dev/null || true`
 
   If the command succeeds and the JSON result contains a non-empty string, display it as a one-line notice. Proceed regardless of outcome.
 
@@ -50,7 +50,7 @@ body: |
 
   ### Step 1.5: Load State and Show Resumption Context
 
-  {{TOOL_PREFIX "Loading colony state..."}} `bash .aether/aether-utils.sh load-state`
+  {{TOOL_PREFIX "Loading colony state..."}} `aether load-state`
 
   If successful and goal is not null:
   1. Extract current_phase from state
@@ -68,7 +68,7 @@ body: |
      - Read .aether/HANDOFF.md content for additional context
      - Remove .aether/HANDOFF.md after displaying (cleanup)
 
-  {{TOOL_PREFIX "Releasing colony lock..."}} `bash .aether/aether-utils.sh unload-state` to release lock.
+  {{TOOL_PREFIX "Releasing colony lock..."}} `aether unload-state` to release lock.
 
   ### Step 2: Compute Summary
 
@@ -116,7 +116,7 @@ body: |
 
   Run using the Bash tool with description "Reading colony depth...":
   ```bash
-  depth_result=$(bash .aether/aether-utils.sh colony-depth get 2>/dev/null || echo '{"ok":true,"result":{"depth":"standard","source":"default"}}')
+  depth_result=$(aether colony-depth get 2>/dev/null || echo '{"ok":true,"result":{"depth":"standard","source":"default"}}')
   colony_depth=$(echo "$depth_result" | jq -r '.result.depth // "standard"')
   depth_source=$(echo "$depth_result" | jq -r '.result.source // "default"')
   echo "colony_depth=$colony_depth"
@@ -150,7 +150,7 @@ body: |
   - Constraints count: `constraints.length`
 
   **Flags:**
-  {{TOOL_PREFIX "Checking for blockers..."}} `bash .aether/aether-utils.sh flag-check-blockers`
+  {{TOOL_PREFIX "Checking for blockers..."}} `aether flag-check-blockers`
   Extract:
   - Blockers count (critical, block advancement)
   - Issues count (high, warnings)
@@ -161,7 +161,7 @@ body: |
 
   {{TOOL_PREFIX "Checking escalation state..."}}
   ```bash
-  escalated_count=$(bash .aether/aether-utils.sh flag-list --type blocker 2>/dev/null | jq '[.result.flags[] | select(.source == "escalation")] | length' 2>/dev/null || echo "0")
+  escalated_count=$(aether flag-list --type blocker --json 2>/dev/null | jq '[.result.flags[] | select(.source == "escalation")] | length' 2>/dev/null || echo "0")
   echo "escalated_count=$escalated_count"
   ```
 
@@ -180,7 +180,7 @@ body: |
 
   ### Step 2.6: Detect Milestone
 
-  {{TOOL_PREFIX "Detecting colony milestone..."}} `bash .aether/aether-utils.sh milestone-detect`
+  {{TOOL_PREFIX "Detecting colony milestone..."}} `aether milestone-detect`
 
   Extract from JSON result:
   - `milestone`: Current milestone name
@@ -192,7 +192,7 @@ body: |
 
   {{TOOL_PREFIX "Loading memory health metrics..."}}
   ```bash
-  bash .aether/aether-utils.sh memory-metrics
+  aether memory-metrics
   ```
 
   Extract from JSON result:
@@ -226,8 +226,8 @@ body: |
   fi
 
   # Generate progress bars
-  phase_bar=$(bash .aether/aether-utils.sh generate-progress-bar "$current_phase" "$total_phases" 20)
-  task_bar=$(bash .aether/aether-utils.sh generate-progress-bar "$tasks_completed" "$tasks_total" 20)
+  phase_bar=$(aether generate-progress-bar "$current_phase" "$total_phases" 20)
+  task_bar=$(aether generate-progress-bar "$tasks_completed" "$tasks_total" 20)
 
   echo "phase_bar=$phase_bar"
   echo "task_bar=$task_bar"
@@ -303,7 +303,7 @@ body: |
   **Colony Vital Signs:**
   After the Memory Health table, run:
   ```bash
-  bash .aether/aether-utils.sh colony-vital-signs
+  aether colony-vital-signs
   ```
 
   Extract from JSON result:
@@ -347,7 +347,7 @@ body: |
   **Data Safety:**
   After the Colony Vital Signs panel, run:
   ```bash
-  bash .aether/aether-utils.sh data-safety-stats
+  aether data-safety-stats
   ```
 
   If the result contains non-zero counts, display:
@@ -365,7 +365,7 @@ body: |
   **Pheromone Summary:**
   After the Data Safety section, run:
   ```bash
-  bash .aether/aether-utils.sh pheromone-count
+  aether pheromone-count
   ```
 
   Display:
@@ -402,7 +402,7 @@ body: |
   current_phase=$(jq -r '.current_phase // 0' .aether/data/COLONY_STATE.json)
   total_phases=$(jq -r '.plan.phases | length' .aether/data/COLONY_STATE.json)
 
-  bash .aether/aether-utils.sh print-next-up "$state" "$current_phase" "$total_phases"
+  aether print-next-up
   ```
 
   This auto-generates state-based recommendations (IDLE → init, READY → build, EXECUTING → continue, PLANNING → plan).

package/.aether/commands/swarm.yaml

@@ -57,7 +57,7 @@ body_claude: |
 
   Initialize swarm findings:
   ```bash
-  bash .aether/aether-utils.sh swarm-findings-init "<swarm_id>"
+  aether swarm-findings-init --id "<swarm_id>"
   ```
 
   #### Step 2.5: Check for Stale Swarm Session
@@ -69,19 +69,19 @@ body_claude: |
 
   Check for stale swarm files:
   ```bash
-  stale_check=$(bash .aether/aether-utils.sh session-verify-fresh --command swarm "" "$SWARM_START")
+  stale_check=$(aether session-verify-fresh --command swarm "" "$SWARM_START")
   has_stale=$(echo "$stale_check" | jq -r '.stale | length')
 
   if [[ "$has_stale" -gt 0 ]]; then
     # Auto-clear stale swarm findings (safe - findings are temporary)
-    bash .aether/aether-utils.sh session-clear --command swarm
+    aether session-clear --command swarm
     echo "Cleared stale swarm findings for fresh investigation"
   fi
   ```
 
   After initializing findings, verify swarm files are fresh:
   ```bash
-  verify_result=$(bash .aether/aether-utils.sh session-verify-fresh --command swarm "" "$SWARM_START")
+  verify_result=$(aether session-verify-fresh --command swarm "" "$SWARM_START")
   if [[ $(echo "$verify_result" | jq -r '.missing | length') -gt 0 ]]; then
     echo "Warning: Swarm files not properly initialized"
   fi
@@ -103,7 +103,7 @@ body_claude: |
 
   Before any investigation that might lead to fixes, run using the Bash tool:
   ```bash
-  bash .aether/aether-utils.sh autofix-checkpoint "pre-swarm-$SWARM_ID"
+  aether autofix-checkpoint --name "pre-swarm-$SWARM_ID"
   ```
 
   Store the result for potential rollback:
@@ -118,7 +118,7 @@ body_claude: |
 
   Read existing blockers for context:
   ```bash
-  bash .aether/aether-utils.sh flag-list --type blocker
+  aether flag-list --type blocker --json
   ```
 
   Read recent activity:
@@ -206,7 +206,7 @@ body_claude: |
 
   As each scout returns, add their findings:
   ```bash
-  bash .aether/aether-utils.sh swarm-findings-add "{swarm_id}" "{scout_type}" "{confidence}" '{finding_json}'
+  aether swarm-findings-add "{swarm_id}" "{scout_type}" "{confidence}" '{finding_json}'
   ```
 
   Display each scout's report as they complete:
@@ -235,7 +235,7 @@ body_claude: |
   Rank fix options:
   ```
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
-                S O L U T I O N   R A N K I N G
+  🏆 S O L U T I O N   R A N K I N G
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
 
   #1 [0.85 confidence] {best solution}
@@ -291,8 +291,8 @@ body_claude: |
 
   Set solution in swarm findings and log success:
   ```bash
-  bash .aether/aether-utils.sh swarm-solution-set "{swarm_id}" '{solution_json}'
-  bash .aether/aether-utils.sh activity-log "SWARM_SUCCESS" "Queen" "Swarm {swarm_id} fixed: {brief description}"
+  aether swarm-solution-set "{swarm_id}" '{solution_json}'
+  aether activity-log "SWARM_SUCCESS" "Queen" "Swarm {swarm_id} fixed: {brief description}"
   ```
 
   **If verification fails:**
@@ -307,8 +307,8 @@ body_claude: |
 
   Rollback and log failure:
   ```bash
-  bash .aether/aether-utils.sh autofix-rollback "{checkpoint_type}" "{checkpoint_ref}"
-  bash .aether/aether-utils.sh activity-log "SWARM_FAILED" "Queen" "Swarm {swarm_id} fix failed verification"
+  aether autofix-rollback --type "{checkpoint_type}" --ref "{checkpoint_ref}"
+  aether activity-log "SWARM_FAILED" "Queen" "Swarm {swarm_id} fix failed verification"
   ```
 
   Track attempt count. If this is the 3rd failure on the same issue:
@@ -334,7 +334,7 @@ body_claude: |
 
   Archive findings:
   ```bash
-  bash .aether/aether-utils.sh swarm-cleanup "{swarm_id}" --archive
+  aether swarm-cleanup "{swarm_id}" --archive
   ```
 
   Generate the state-based Next Up block:
@@ -342,7 +342,7 @@ body_claude: |
   state=$(jq -r '.state // "IDLE"' .aether/data/COLONY_STATE.json)
   current_phase=$(jq -r '.current_phase // 0' .aether/data/COLONY_STATE.json)
   total_phases=$(jq -r '.plan.phases | length' .aether/data/COLONY_STATE.json)
-  bash .aether/aether-utils.sh print-next-up "$state" "$current_phase" "$total_phases"
+  aether print-next-up
   ```
 
 body_opencode: |

package/.aether/commands/tunnels.yaml

@@ -28,7 +28,7 @@ body_claude: |
 
   ### Step 2: List All Chambers
 
-  Run using the Bash tool with description "Loading chamber list...": `bash .aether/aether-utils.sh chamber-list`
+  Run using the Bash tool with description "Loading chamber list...": `aether chamber-list`
 
   Parse JSON result into array of chambers.
 
@@ -126,7 +126,7 @@ body_claude: |
   ```
 
   To get the hash status, run using the Bash tool with description "Verifying chamber integrity...":
-  - Run `bash .aether/aether-utils.sh chamber-verify .aether/chambers/{chamber_name}`
+  - Run `aether chamber-verify --path .aether/chambers/{chamber_name}`
   - If verified: hash_status = "verified"
   - If not verified: hash_status = "hash mismatch"
   - If error: hash_status = "error"
@@ -341,7 +341,7 @@ body_claude: |
   # Import the EXTRACTED pheromone-only XML (NOT the combined colony-archive.xml)
   # $import_tmp_pheromones has <pheromones> as root — the format pheromone-import-xml expects
   # Second argument triggers prefix-tagging — imported signal IDs become "{source_colony}:original_id"
-  import_result=$(bash .aether/aether-utils.sh pheromone-import-xml "$import_tmp_pheromones" "$source_colony" 2>&1)
+  import_result=$(aether pheromone-import-xml --input "$import_tmp_pheromones" --colony "$source_colony" 2>&1)
   import_ok=$(echo "$import_result" | jq -r '.ok // false' 2>/dev/null)
 
   if [[ "$import_ok" == "true" ]]; then
@@ -394,7 +394,7 @@ body_claude: |
   state=$(jq -r '.state // "IDLE"' .aether/data/COLONY_STATE.json)
   current_phase=$(jq -r '.current_phase // 0' .aether/data/COLONY_STATE.json)
   total_phases=$(jq -r '.plan.phases | length' .aether/data/COLONY_STATE.json)
-  bash .aether/aether-utils.sh print-next-up "$state" "$current_phase" "$total_phases"
+  aether print-next-up
   ```
 
   ## Implementation Notes
@@ -445,7 +445,7 @@ body_opencode: |
 
   ### Step 2: List All Chambers
 
-  Run: `bash .aether/aether-utils.sh chamber-list`
+  Run: `aether chamber-list`
 
   Parse JSON result into array of chambers.
 
@@ -508,7 +508,7 @@ body_opencode: |
   ```
 
   To get the counts and hash status:
-  - Run `bash .aether/aether-utils.sh chamber-verify .aether/chambers/{chamber_name}`
+  - Run `aether chamber-verify --path .aether/chambers/{chamber_name}`
   - If verified: hash_status = "✅"
   - If not verified: hash_status = "⚠️ hash mismatch"
   - If error: hash_status = "⚠️ error"
@@ -751,7 +751,7 @@ body_opencode: |
   # Import the EXTRACTED pheromone-only XML (NOT the combined colony-archive.xml)
   # $import_tmp_pheromones has <pheromones> as root — the format pheromone-import-xml expects
   # Second argument triggers prefix-tagging — imported signal IDs become "{source_colony}:original_id"
-  import_result=$(bash .aether/aether-utils.sh pheromone-import-xml "$import_tmp_pheromones" "$source_colony" 2>&1)
+  import_result=$(aether pheromone-import-xml --input "$import_tmp_pheromones" --colony "$source_colony" 2>&1)
   import_ok=$(echo "$import_result" | jq -r '.ok // false' 2>/dev/null)
 
   if [[ "$import_ok" == "true" ]]; then

package/.aether/commands/update.yaml

@@ -126,6 +126,6 @@ body: |
   state=$(jq -r '.state // "IDLE"' .aether/data/COLONY_STATE.json)
   current_phase=$(jq -r '.current_phase // 0' .aether/data/COLONY_STATE.json)
   total_phases=$(jq -r '.plan.phases | length' .aether/data/COLONY_STATE.json)
-  bash .aether/aether-utils.sh print-next-up "$state" "$current_phase" "$total_phases"
+  aether print-next-up
   ```
   {{/claude}}

package/.aether/commands/verify-castes.yaml

@@ -65,10 +65,10 @@ body: |
   ## Step 2: Check System Status
 
   {{#claude}}
-  Run using the Bash tool with description "Checking colony version...": `bash .aether/aether-utils.sh version-check-cached 2>/dev/null || echo "Utils available"`
+  Run using the Bash tool with description "Checking colony version...": `aether version-check-cached 2>/dev/null || echo "Utils available"`
   {{/claude}}
   {{#opencode}}
-  Run using Bash tool: `bash .aether/aether-utils.sh version-check 2>/dev/null || echo "Utils available"`
+  Run using Bash tool: `aether version-check-cached 2>/dev/null || echo "Utils available"`
   {{/opencode}}
 
   Check LiteLLM proxy status:
@@ -138,7 +138,7 @@ body: |
   state=$(jq -r '.state // "IDLE"' .aether/data/COLONY_STATE.json)
   current_phase=$(jq -r '.current_phase // 0' .aether/data/COLONY_STATE.json)
   total_phases=$(jq -r '.plan.phases | length' .aether/data/COLONY_STATE.json)
-  bash .aether/aether-utils.sh print-next-up "$state" "$current_phase" "$total_phases"
+  aether print-next-up
   ```
   {{/claude}}