aether-colony 5.3.3 → 5.4.0

package/.aether/commands/continue.yaml

@@ -84,7 +84,7 @@ body_opencode: |
 
   ### Step 1.5: Load State and Show Resumption Context
 
-  Run using Bash tool: `bash .aether/aether-utils.sh load-state`
+  Run using Bash tool: `aether load-state`
 
   If successful and goal is not null:
   1. Extract current_phase from state
@@ -99,7 +99,7 @@ body_opencode: |
   - Read .aether/HANDOFF.md for additional context
   - Remove .aether/HANDOFF.md after display (cleanup)
 
-  Run: `bash .aether/aether-utils.sh unload-state` to release lock.
+  Run: `aether unload-state` to release lock.
 
   **Error handling:**
   - If E_FILE_NOT_FOUND: "No colony initialized. Run /ant:init first." and stop
@@ -125,7 +125,7 @@ body_opencode: |
 
   Run:
   ```bash
-  survey_check=$(bash .aether/aether-utils.sh survey-verify 2>/dev/null || true)
+  survey_check=$(aether survey-verify 2>/dev/null || true)
   survey_docs=$(ls -1 .aether/data/survey/*.md 2>/dev/null | wc -l | tr -d ' ')
   survey_latest=$(ls -t .aether/data/survey/*.md 2>/dev/null | head -1)
   if [[ -n "$survey_latest" ]]; then
@@ -234,7 +234,7 @@ body_opencode: |
   3. **If spawning Probe:**
 
      a. Generate Probe name and dispatch:
-     Run using the Bash tool with description "Generating Probe name...": `probe_name=$(bash .aether/aether-utils.sh generate-ant-name "probe") && bash .aether/aether-utils.sh spawn-log "Queen" "probe" "$probe_name" "Coverage improvement: ${coverage_percent}%" && echo "{\"name\":\"$probe_name\"}"`
+     Run using the Bash tool with description "Generating Probe name...": `probe_name=$(aether generate-ant-name --caste "probe") && aether spawn-log --name "Queen" --caste "probe" --id "$probe_name" --description "Coverage improvement: ${coverage_percent}%" && echo "{\"name\":\"$probe_name\"}"`
 
      b. Display:
      ```
@@ -264,10 +264,10 @@ body_opencode: |
      f. Parse Probe JSON output and log completion:
      Extract: `tests_added`, `coverage.lines`, `coverage.branches`, `coverage.functions`, `edge_cases_discovered`
 
-     Run using the Bash tool with description "Logging Probe completion...": `bash .aether/aether-utils.sh spawn-complete "$probe_name" "completed" "{probe_summary}"`
+     Run using the Bash tool with description "Logging Probe completion...": `aether spawn-complete --id "$probe_name" --status "completed" --summary "{probe_summary}"`
 
      g. Log findings to midden:
-     Run using the Bash tool with description "Logging Probe findings to midden...": `bash .aether/aether-utils.sh midden-write "coverage" "Probe generated tests, coverage: ${coverage_lines}%/${coverage_branches}%/${coverage_functions}%" "probe"`
+     Run using the Bash tool with description "Logging Probe findings to midden...": `aether midden-write "coverage" "Probe generated tests, coverage: ${coverage_lines}%/${coverage_branches}%/${coverage_functions}%" "probe"`
 
   4. **NON-BLOCKING continuation:**
      Display Probe findings summary:
@@ -416,8 +416,8 @@ body_opencode: |
   **CRITICAL:** Do NOT proceed to Step 1.7. Do NOT advance the phase.
   Log the violation:
   ```bash
-  bash .aether/aether-utils.sh activity-log "BLOCKED" "colony" "Spawn gate failed: {task_count} tasks, 0 spawns"
-  bash .aether/aether-utils.sh error-flag-pattern "no-spawn-violation" "Prime Worker completed phase without spawning specialists" "critical"
+  aether activity-log "BLOCKED" "colony" "Spawn gate failed: {task_count} tasks, 0 spawns"
+  aether error-flag-pattern "no-spawn-violation" "Prime Worker completed phase without spawning specialists" "critical"
   ```
 
   **HARD REJECTION - If watcher_count == 0 (no testing separation):**
@@ -458,7 +458,7 @@ body_opencode: |
   Scan all modified/created files for known anti-patterns. This catches recurring bugs before they reach production.
 
   ```bash
-  bash .aether/aether-utils.sh check-antipattern "{file_path}"
+  aether check-antipattern "{file_path}"
   ```
 
   Run for each file in `files_created` and `files_modified` from Prime Worker output.
@@ -567,7 +567,7 @@ body_opencode: |
      Run using the Bash tool with description "Establishing test baseline...": `test_output_before=$(npm test 2>&1 || echo "TEST_FAILED") && tests_passing_before=$(echo "$test_output_before" | grep -oE '[0-9]+ passing' | grep -oE '[0-9]+' || echo "0") && echo "Baseline: $tests_passing_before tests passing"`
 
      b. **Generate Weaver name and dispatch:**
-     Run using the Bash tool with description "Generating Weaver name...": `weaver_name=$(bash .aether/aether-utils.sh generate-ant-name "weaver") && bash .aether/aether-utils.sh spawn-log "Queen" "weaver" "$weaver_name" "Proactive refactoring" && echo "{\"name\":\"$weaver_name\"}"`
+     Run using the Bash tool with description "Generating Weaver name...": `weaver_name=$(aether generate-ant-name --caste "weaver") && aether spawn-log --name "Queen" --caste "weaver" --id "$weaver_name" --description "Proactive refactoring" && echo "{\"name\":\"$weaver_name\"}"`
 
      c. **Display:**
      ```
@@ -613,10 +613,10 @@ body_opencode: |
      ```
 
      g. **Log completion:**
-     Run using the Bash tool with description "Logging Weaver completion...": `bash .aether/aether-utils.sh spawn-complete "$weaver_name" "$weaver_status" "Refactoring $weaver_status"`
+     Run using the Bash tool with description "Logging Weaver completion...": `aether spawn-complete --id "$weaver_name" --status "$weaver_status" --summary "Refactoring $weaver_status"`
 
      h. **Log to midden:**
-     Run using the Bash tool with description "Logging refactoring activity to midden...": `bash .aether/aether-utils.sh midden-write "refactoring" "Weaver refactored files, complexity before/after: ${complexity_before}/${complexity_after}" "weaver"`
+     Run using the Bash tool with description "Logging refactoring activity to midden...": `aether midden-write "refactoring" "Weaver refactored files, complexity before/after: ${complexity_before}/${complexity_after}" "weaver"`
 
   5. **Display completion:**
      ```
@@ -645,7 +645,7 @@ body_opencode: |
   **If package.json exists:**
 
   1. Generate Gatekeeper name and log spawn:
-  Run using the Bash tool with description "Generating Gatekeeper name...": `gatekeeper_name=$(bash .aether/aether-utils.sh generate-ant-name "gatekeeper") && bash .aether/aether-utils.sh spawn-log "Queen" "gatekeeper" "$gatekeeper_name" "Supply chain security audit" && echo "{\"name\":\"$gatekeeper_name\"}"`
+  Run using the Bash tool with description "Generating Gatekeeper name...": `gatekeeper_name=$(aether generate-ant-name --caste "gatekeeper") && aether spawn-log --name "Queen" --caste "gatekeeper" --id "$gatekeeper_name" --description "Supply chain security audit" && echo "{\"name\":\"$gatekeeper_name\"}"`
 
   2. Display:
   ```
@@ -667,7 +667,7 @@ body_opencode: |
   5. Parse Gatekeeper JSON output and log completion:
   Extract: `security.critical`, `security.high`, `status`
 
-  Run using the Bash tool with description "Logging Gatekeeper completion...": `bash .aether/aether-utils.sh spawn-complete "$gatekeeper_name" "completed" "{gatekeeper_summary}"`
+  Run using the Bash tool with description "Logging Gatekeeper completion...": `aether spawn-complete --id "$gatekeeper_name" --status "completed" --summary "{gatekeeper_summary}"`
 
   **Gate Decision Logic:**
 
@@ -695,7 +695,7 @@ body_opencode: |
   Security warnings logged to midden for later review.
   Proceeding with caution...
   ```
-  Run using the Bash tool with description "Logging high-severity warnings...": `bash .aether/aether-utils.sh midden-write "security" "High CVEs found: $high_count" "gatekeeper"`
+  Run using the Bash tool with description "Logging high-severity warnings...": `aether midden-write "security" "High CVEs found: $high_count" "gatekeeper"`
   Continue to Step 1.9.
 
   - **If clean (no critical or high):**
@@ -709,7 +709,7 @@ body_opencode: |
   **Code quality audit -- runs on every `/ant:continue` for consistent coverage.**
 
   1. Generate Auditor name and log spawn:
-  Run using the Bash tool with description "Generating Auditor name...": `auditor_name=$(bash .aether/aether-utils.sh generate-ant-name "auditor") && bash .aether/aether-utils.sh spawn-log "Queen" "auditor" "$auditor_name" "Code quality audit" && echo "{\"name\":\"$auditor_name\"}"`
+  Run using the Bash tool with description "Generating Auditor name...": `auditor_name=$(aether generate-ant-name --caste "auditor") && aether spawn-log --name "Queen" --caste "auditor" --id "$auditor_name" --description "Code quality audit" && echo "{\"name\":\"$auditor_name\"}"`
 
   2. Display:
   ```
@@ -734,7 +734,7 @@ body_opencode: |
   6. Parse Auditor JSON output and log completion:
   Extract: `findings.critical`, `findings.high`, `findings.medium`, `findings.low`, `findings.info`, `overall_score`, `dimensions_audited`
 
-  Run using the Bash tool with description "Logging Auditor completion...": `bash .aether/aether-utils.sh spawn-complete "$auditor_name" "completed" "{auditor_summary}"`
+  Run using the Bash tool with description "Logging Auditor completion...": `aether spawn-complete --id "$auditor_name" --status "completed" --summary "{auditor_summary}"`
 
   **Gate Decision Logic:**
 
@@ -756,7 +756,7 @@ body_opencode: |
 
   The phase will NOT advance with critical quality issues.
   ```
-  Run using the Bash tool with description "Logging critical quality block...": `bash .aether/aether-utils.sh error-flag-pattern "auditor-critical-findings" "$critical_count critical quality issues found" "critical"`
+  Run using the Bash tool with description "Logging critical quality block...": `aether error-flag-pattern "auditor-critical-findings" "$critical_count critical quality issues found" "critical"`
   **CRITICAL:** Do NOT proceed to Step 1.10. Stop here.
 
   - **Else if `overall_score < 60`:**
@@ -774,7 +774,7 @@ body_opencode: |
 
   The phase will NOT advance with quality score below 60.
   ```
-  Run using the Bash tool with description "Logging quality score block...": `bash .aether/aether-utils.sh error-flag-pattern "auditor-quality-score" "Score $overall_score below threshold 60" "critical"`
+  Run using the Bash tool with description "Logging quality score block...": `aether error-flag-pattern "auditor-quality-score" "Score $overall_score below threshold 60" "critical"`
   **CRITICAL:** Do NOT proceed to Step 1.10. Stop here.
 
   - **Else if `findings.high > 0`:**
@@ -787,7 +787,7 @@ body_opencode: |
   Quality warnings logged to midden for later review.
   Proceeding with caution...
   ```
-  Run using the Bash tool with description "Logging high-quality warnings...": `bash .aether/aether-utils.sh midden-write "quality" "High severity issues: $high_count (score: $overall_score)" "auditor"`
+  Run using the Bash tool with description "Logging high-quality warnings...": `aether midden-write "quality" "High severity issues: $high_count (score: $overall_score)" "auditor"`
   Continue to Step 1.10.
 
   - **If clean (score >= 60, no critical):**
@@ -833,7 +833,7 @@ body_opencode: |
 
   **CRITICAL:** Do NOT proceed. Log the violation:
   ```bash
-  bash .aether/aether-utils.sh error-flag-pattern "fabricated-tdd" "Prime Worker reported TDD metrics without creating test files" "critical"
+  aether error-flag-pattern "fabricated-tdd" "Prime Worker reported TDD metrics without creating test files" "critical"
   ```
 
   **If tests_added == 0 or test files exist matching claims:**
@@ -879,7 +879,7 @@ body_opencode: |
 
   Use AskUserQuestion to get issue details. Log to errors.records:
   ```bash
-  bash .aether/aether-utils.sh error-add "runtime" "critical" "{user_description}" {phase}
+  aether error-add "runtime" "critical" "{user_description}" {phase}
   ```
 
   Do NOT proceed to Step 2.
@@ -915,12 +915,12 @@ body_opencode: |
 
   First, auto-resolve any flags eligible for resolution now that verification has passed:
   ```bash
-  bash .aether/aether-utils.sh flag-auto-resolve "build_pass"
+  aether flag-auto-resolve "build_pass"
   ```
 
   Then check for remaining blocking flags:
   ```bash
-  bash .aether/aether-utils.sh flag-check-blockers {current_phase}
+  aether flag-check-blockers {current_phase}
   ```
 
   Parse result for `blockers`, `issues`, and `notes` counts.
@@ -1022,7 +1022,7 @@ body_opencode: |
 
      Run using the Bash tool with description "Recording learning observations...":
      ```bash
-     colony_name=$(bash .aether/aether-utils.sh colony-name 2>/dev/null | jq -r '.result.name // ""')
+     colony_name=$(aether colony-name 2>/dev/null | jq -r '.result.name // ""')
      [[ -z "$colony_name" ]] && colony_name="unknown"
 
      # Get learnings from the current phase
@@ -1032,7 +1032,7 @@ body_opencode: |
        echo "$current_phase_learnings" | jq -r '.learnings[]?.claim // empty' 2>/dev/null | while read -r claim; do
          if [[ -n "$claim" ]]; then
            # Default wisdom_type to "pattern" (threshold: 3 observations)
-           bash .aether/aether-utils.sh memory-capture "learning" "$claim" "pattern" "worker:continue" 2>/dev/null || true
+           aether memory-capture "learning" "$claim" "pattern" "worker:continue" 2>/dev/null || true
          fi
        done
        echo "Recorded observations for threshold tracking"
@@ -1108,7 +1108,7 @@ body_opencode: |
   Write COLONY_STATE.json.
 
   Validate the state file:
-  Run using the Bash tool with description "Validating colony state...": `bash .aether/aether-utils.sh validate-state colony`
+  Run using the Bash tool with description "Validating colony state...": `aether validate-state colony`
 
   ### Step 2.1: Auto-Emit Phase Pheromones (SILENT)
 
@@ -1126,7 +1126,7 @@ body_opencode: |
   phase_feedback="Phase $phase_id ($phase_name) completed. Key patterns: {brief summary of 1-3 learnings from Step 2}"
   # Fallback if no learnings: "Phase $phase_id ($phase_name) completed without notable patterns."
 
-  bash .aether/aether-utils.sh pheromone-write FEEDBACK "$phase_feedback" \
+  aether pheromone-write --type FEEDBACK --content "$phase_feedback" \
     --strength 0.6 \
     --source "worker:continue" \
     --reason "Auto-emitted on phase advance: captures what worked and what was learned" \
@@ -1146,7 +1146,7 @@ body_opencode: |
   For each pattern returned by the above query, emit a REDIRECT signal:
 
   ```bash
-  bash .aether/aether-utils.sh pheromone-write REDIRECT "$pattern_text" \
+  aether pheromone-write --type REDIRECT --content "$pattern_text" \
     --strength 0.7 \
     --source "system" \
     --reason "Auto-emitted: error pattern recurred across 2+ phases" \
@@ -1156,7 +1156,7 @@ body_opencode: |
   Also capture each recurring pattern as a resolution candidate:
 
   ```bash
-  bash .aether/aether-utils.sh memory-capture \
+  aether memory-capture \
     "resolution" \
     "$pattern_text" \
     "pattern" \
@@ -1169,7 +1169,7 @@ body_opencode: |
 
   After auto-emission, expire all signals with `expires_at == "phase_end"`:
 
-  Run using the Bash tool with description "Maintaining pheromone memory...": `bash .aether/aether-utils.sh pheromone-expire --phase-end-only 2>/dev/null && bash .aether/aether-utils.sh eternal-init 2>/dev/null`
+  Run using the Bash tool with description "Maintaining pheromone memory...": `aether pheromone-expire --phase-end-only 2>/dev/null && aether eternal-init 2>/dev/null`
 
   ### Step 2.1.5: Check for Promotion Proposals
 
@@ -1179,7 +1179,7 @@ body_opencode: |
 
   1. **Check for proposals:**
      ```bash
-     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')
      ```
 
@@ -1189,7 +1189,7 @@ body_opencode: |
 
      ```bash
      if [[ "$proposal_count" -gt 0 ]]; then
-       bash .aether/aether-utils.sh learning-approve-proposals
+       aether learning-approve-proposals
      fi
      # If no proposals, silently skip without notice
      ```
@@ -1258,7 +1258,7 @@ body_opencode: |
   **Step 2.3.1: Collect plan data**
 
   ```bash
-  bash .aether/aether-utils.sh changelog-collect-plan-data "{phase_identifier}" "{plan_number}"
+  aether changelog-collect-plan-data "{phase_identifier}" "{plan_number}"
   ```
 
   Parse the returned JSON to extract `files`, `decisions`, `worked`, and `requirements` arrays.
@@ -1274,7 +1274,7 @@ body_opencode: |
   **Step 2.3.2: Append changelog entry**
 
   ```bash
-  bash .aether/aether-utils.sh changelog-append \
+  aether changelog-append \
     "$(date +%Y-%m-%d)" \
     "{phase_identifier}" \
     "{plan_number}" \
@@ -1296,7 +1296,7 @@ body_opencode: |
 
   1. **Generate the commit message:**
   ```bash
-  bash .aether/aether-utils.sh generate-commit-message "milestone" {phase_id} "{phase_name}" "{one_line_summary}"
+  aether generate-commit-message --type "milestone" --phase {phase_id} --subject "{phase_name}" "{one_line_summary}"
   ```
   Parse the returned JSON to extract `message` and `files_changed`.
 
@@ -1397,18 +1397,18 @@ body_opencode: |
 
   **Log the activity:**
   ```bash
-  bash .aether/aether-utils.sh context-update activity "continue" "Phase {prev_id} completed, advanced to {next_id}" "---"
+  aether context-update activity "continue" "Phase {prev_id} completed, advanced to {next_id}" "---"
   ```
 
   **Update the phase:**
   ```bash
-  bash .aether/aether-utils.sh context-update update-phase {next_id} "{next_phase_name}" "YES" "Phase advanced, ready to build"
+  aether context-update update-phase {next_id} "{next_phase_name}" "YES" "Phase advanced, ready to build"
   ```
 
   **Log any decisions from this session:**
   If any architectural decisions were made during verification, also run:
   ```bash
-  bash .aether/aether-utils.sh context-update decision "{decision_description}" "{rationale}" "Queen"
+  aether context-update decision "{decision_description}" "{rationale}" "Queen"
   ```
 
   ### Step 2.7: Project Completion
@@ -1480,5 +1480,5 @@ body_opencode: |
 
   Update the session tracking file to enable `/ant:resume` after context clear:
 
-  Run using the Bash tool with description "Saving session state...": `bash .aether/aether-utils.sh session-update "/ant:continue" "/ant:build {next_id}" "Phase {prev_id} completed, advanced to Phase {next_id}"`
+  Run using the Bash tool with description "Saving session state...": `aether session-update --command "/ant:continue" --worker "/ant:build {next_id}" --summary "Phase {prev_id} completed, advanced to Phase {next_id}"`
 

package/.aether/commands/council.yaml

@@ -22,7 +22,7 @@ body: |
 
   Run using the Bash tool with description "Checking deliberation budget...":
   ```bash
-  bash .aether/aether-utils.sh council-budget-check
+  aether council-budget-check
   ```
 
   Parse result. If `allowed` is `false`:
@@ -38,7 +38,7 @@ body: |
 
   Run using the Bash tool with description "Opening deliberation...":
   ```bash
-  bash .aether/aether-utils.sh council-deliberate --proposal "<proposal>"
+  aether council-deliberate --proposal "<proposal>"
   ```
 
   Capture `deliberation_id` from `result.id`.
@@ -81,7 +81,7 @@ body: |
 
   Record the argument:
   ```bash
-  bash .aether/aether-utils.sh council-advocate \
+  aether council-advocate \
     --deliberation-id "<deliberation_id>" \
     --argument "<advocate_argument>"
   ```
@@ -119,7 +119,7 @@ body: |
 
   Record the argument:
   ```bash
-  bash .aether/aether-utils.sh council-challenger \
+  aether council-challenger \
     --deliberation-id "<deliberation_id>" \
     --argument "<challenger_argument>"
   ```
@@ -162,7 +162,7 @@ body: |
 
   Record the sage synthesis:
   ```bash
-  bash .aether/aether-utils.sh council-sage \
+  aether council-sage \
     --deliberation-id "<deliberation_id>" \
     --synthesis "<synthesis>" \
     --recommendation "<recommendation>"
@@ -504,6 +504,6 @@ 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/data-clean.yaml

@@ -16,7 +16,7 @@ body: |
 
   Run using the Bash tool with description "Scanning colony data for test artifacts...":
   ```bash
-  bash .aether/aether-utils.sh data-clean --dry-run
+  aether data-clean --dry-run
   ```
 
   Display the output to the user. This shows artifact counts per data file without modifying anything.
@@ -45,7 +45,7 @@ body: |
 
   If user confirmed, run using the Bash tool with description "Removing test artifacts...":
   ```bash
-  bash .aether/aether-utils.sh data-clean --confirm
+  aether data-clean --confirm
   ```
 
   ### Step 4: Summary
@@ -75,6 +75,6 @@ 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/dream.yaml

@@ -234,7 +234,7 @@ body: |
   Run using the Bash tool with description "Logging dream activity...":
   {{/claude}}
   ```bash
-  bash .aether/aether-utils.sh activity-log "DREAM" "Dreamer" "Dream session: {N} observations, {concerns} concerns, {pheromones} pheromone suggestions"
+  aether activity-log "DREAM" "Dreamer" "Dream session: {N} observations, {concerns} concerns, {pheromones} pheromone suggestions"
   ```
 
   {{#claude}}
@@ -243,7 +243,7 @@ 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}}

package/.aether/commands/entomb.yaml

@@ -126,7 +126,7 @@ body_claude: |
 
   ```bash
   # 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
@@ -140,7 +140,7 @@ 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 entombment..."
@@ -202,12 +202,12 @@ body_claude: |
   ```bash
   queen_file=".aether/QUEEN.md"
   if [[ ! -f "$queen_file" ]]; then
-    init_result=$(bash .aether/aether-utils.sh queen-init 2>/dev/null || echo '{"ok":false}')
+    init_result=$(aether queen-init 2>/dev/null || echo '{"ok":false}')
     init_ok=$(echo "$init_result" | jq -r '.ok // false')
     if [[ "$init_ok" == "true" ]]; then
       created=$(echo "$init_result" | jq -r '.result.created // false')
       if [[ "$created" == "true" ]]; then
-        bash .aether/aether-utils.sh activity-log "CREATED" "Queen" "Initialized QUEEN.md for wisdom storage"
+        aether activity-log "CREATED" "Queen" "Initialized QUEEN.md for wisdom storage"
       fi
     fi
   fi
@@ -245,7 +245,7 @@ body_claude: |
 
   Create the chamber:
   ```bash
-  bash .aether/aether-utils.sh chamber-create \
+  aether chamber-create \
     ".aether/chambers/$chamber_name" \
     ".aether/data/COLONY_STATE.json" \
     "$goal" \
@@ -295,7 +295,7 @@ body_claude: |
 
   ```bash
   chamber_dir=".aether/chambers/$chamber_name"
-  xml_result=$(bash .aether/aether-utils.sh colony-archive-xml "$chamber_dir/colony-archive.xml" 2>&1)
+  xml_result=$(aether colony-archive-xml --output "$chamber_dir/colony-archive.xml" 2>&1)
   xml_ok=$(echo "$xml_result" | jq -r '.ok // false' 2>/dev/null)
 
   if [[ "$xml_ok" != "true" ]]; then
@@ -323,7 +323,7 @@ body_claude: |
 
   Run verification:
   ```bash
-  bash .aether/aether-utils.sh chamber-verify ".aether/chambers/$chamber_name"
+  aether chamber-verify --path ".aether/chambers/$chamber_name"
   ```
 
   If verification fails, display error and stop:
@@ -341,7 +341,7 @@ body_claude: |
 
   Write colony summary to eternal memory:
   ```bash
-  bash .aether/aether-utils.sh eternal-init  # idempotent
+  aether eternal-init  # idempotent
   eternal_file="$HOME/.aether/eternal/memory.json"
   if [[ -f "$eternal_file" ]]; then
     colony_entry=$(jq -n \
@@ -679,7 +679,7 @@ body_opencode: |
 
   Create the chamber:
   ```bash
-  bash .aether/aether-utils.sh chamber-create \
+  aether chamber-create \
     ".aether/chambers/{chamber_name}" \
     ".aether/data/COLONY_STATE.json" \
     "{goal}" \
@@ -697,7 +697,7 @@ body_opencode: |
 
   ```bash
   chamber_dir=".aether/chambers/$chamber_name"
-  xml_result=$(bash .aether/aether-utils.sh colony-archive-xml "$chamber_dir/colony-archive.xml" 2>&1)
+  xml_result=$(aether colony-archive-xml --output "$chamber_dir/colony-archive.xml" 2>&1)
   xml_ok=$(echo "$xml_result" | jq -r '.ok // false' 2>/dev/null)
 
   if [[ "$xml_ok" != "true" ]]; then
@@ -733,7 +733,7 @@ body_opencode: |
 
   Run verification:
   ```bash
-  bash .aether/aether-utils.sh chamber-verify ".aether/chambers/{chamber_name}"
+  aether chamber-verify --path ".aether/chambers/{chamber_name}"
   ```
 
   If verification fails, display error and stop:

package/.aether/commands/export-signals.yaml

@@ -20,7 +20,7 @@ body: |
 
   Run using the Bash tool with description "Exporting pheromone signals to XML...":
   ```bash
-  bash .aether/aether-utils.sh pheromone-export-xml "<output_path>"
+  aether pheromone-export-xml --output "<output_path>"
   ```
 
   Parse the returned JSON:
@@ -59,6 +59,6 @@ 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/feedback.yaml

@@ -32,7 +32,7 @@ body: |
   {{#claude}}
   {{TOOL_PREFIX "Recording colony feedback..."}}
   ```bash
-  bash .aether/aether-utils.sh pheromone-write FEEDBACK "<content>" --strength 0.7 --reason "User feedback guidance" --ttl <ttl>
+  aether pheromone-write --type FEEDBACK --content "<content>" --strength 0.7 --reason "User feedback guidance" --ttl <ttl>
   ```
 
   **Create instinct from feedback:**
@@ -59,14 +59,14 @@ body: |
 
   {{TOOL_PREFIX "Updating context document..."}}
   ```bash
-  bash .aether/aether-utils.sh context-update constraint feedback "<content>" "user" 2>/dev/null || true
+  aether context-update --section constraint --key feedback --content "<content>" "user" 2>/dev/null || true
   ```
 
   ### Step 3: Get Active Counts
 
   {{TOOL_PREFIX "Counting active signals..."}}
   ```bash
-  bash .aether/aether-utils.sh pheromone-count
+  aether pheromone-count
   ```
 
   ### Step 4: Confirm
@@ -119,8 +119,8 @@ body: |
 
   **Write pheromone signal and update context:**
   ```bash
-  bash .aether/aether-utils.sh pheromone-write FEEDBACK "$normalized_args" --strength 0.7 --reason "User feedback guidance" 2>/dev/null || true
-  bash .aether/aether-utils.sh context-update constraint feedback "$normalized_args" "user" 2>/dev/null || true
+  aether pheromone-write --type FEEDBACK --content "$normalized_args" --strength 0.7 --reason "User feedback guidance" 2>/dev/null || true
+  aether context-update --section constraint --key feedback --content "$normalized_args" "user" 2>/dev/null || true
   ```
 
   ### Step 3: Confirm
@@ -153,6 +153,6 @@ 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/flag.yaml

@@ -48,7 +48,7 @@ body: |
 
   {{TOOL_PREFIX "Raising colony flag..."}}
   ```bash
-  bash .aether/aether-utils.sh flag-add "{type}" "{title}" "{description}" "manual" {phase_or_null}
+  aether flag-add --severity "{type}" --title "{title}" --description "{description}" --source "manual" --phase {phase_or_null}
   ```
 
   Parse the result for the flag ID.
@@ -144,7 +144,7 @@ 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}}
 

package/.aether/commands/flags.yaml

@@ -32,7 +32,7 @@ body: |
   If `--resolve` was provided:
   {{/opencode}}
   ```bash
-  bash .aether/aether-utils.sh flag-resolve "{flag_id}" "{resolution_message}"
+  aether flag-resolve --id "{flag_id}" --message "{resolution_message}"
   ```
   Output:
   ```
@@ -49,7 +49,7 @@ body: |
   If `--ack` was provided:
   {{/opencode}}
   ```bash
-  bash .aether/aether-utils.sh flag-acknowledge "{flag_id}"
+  aether flag-acknowledge --id "{flag_id}"
   ```
   Output:
   ```
@@ -68,7 +68,7 @@ body: |
   Run:
   {{/opencode}}
   ```bash
-  bash .aether/aether-utils.sh flag-list {options}
+  aether flag-list {options}
   ```
 
   Parse result for flags array.
@@ -153,7 +153,7 @@ 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}}