diff --git a/claude/aqe-reference.md b/claude/aqe-reference.md
new file mode 100644
index 00000000..58199068
--- /dev/null
+++ b/claude/aqe-reference.md
@@ -0,0 +1,45 @@
+<!-- BEGIN ruflo-aqe-reference -->
+<!-- ruflo-aqe-reference: merged into ~/.claude/CLAUDE.md ONLY when agentic-qe is installed.
+     Managed by install.sh / ruflo-reference-refresh — stripped automatically when `aqe` is
+     absent. Source of truth: claude/aqe-reference.md in the ruflo-machine-ref kit. -->
+
+## Agentic-QE — operating guidance
+
+> Applies when the standalone **agentic-qe** fleet is installed (`aqe` on PATH). This is the
+> reusable subset of what `aqe init` would otherwise append to each project's `CLAUDE.md`;
+> per-project specifics (enabled domains, worker config, the generation timestamp, local
+> `.agentic-qe/` paths) are intentionally **not** here — `aqe init` writes those into the repo.
+
+### Critical policies (apply whenever agentic-qe is in use)
+- **Integrity (absolute):** no shortcuts, fake data, or false success claims; verify before
+  claiming done; use real DB queries in integration tests; run actual tests, don't assume.
+- **Test execution:** never run `npm test` without `--run` (watch-mode hang risk) — use
+  `npm test -- --run`, or `npm run test:unit` / `test:integration` when available.
+- **Data protection:** never `rm -f` `.agentic-qe/` or `*.db` without confirmation; back up
+  before destructive database operations.
+- **Git:** never auto-commit/push without an explicit user request.
+
+### Driving the AQE MCP
+Tools are prefixed `mcp__agentic-qe__` (discover via `ToolSearch`). **`fleet_init` MUST be
+called first**, e.g. `fleet_init({ topology:"hierarchical", maxAgents:15, memoryBackend:"hybrid" })`.
+
+| Tool | Purpose |
+|------|---------|
+| `fleet_init` | Initialize the QE fleet (call first) · `fleet_status` for health |
+| `test_generate_enhanced` | AI-powered test generation (`framework`, `strategy`) |
+| `test_execute_parallel` | Parallel execution with retry |
+| `coverage_analyze_sublinear` | O(log n) coverage analysis (`paths`, `threshold`) |
+| `quality_assess` | Quality-gate evaluation |
+| `task_orchestrate` | Multi-agent QE tasks across domains (`parallel:true`) |
+| `memory_store` / `memory_query` | Patterns with `namespace` + `persist:true` (learning) |
+| `security_scan_comprehensive` | SAST/DAST scanning |
+
+### QE agents via the native Task tool
+QE agents live under `.claude/agents/v3/` once `aqe init` has run in the repo:
+```javascript
+Task({ prompt: "Generate tests",     subagent_type: "qe-test-architect",      run_in_background: true })
+Task({ prompt: "Find coverage gaps", subagent_type: "qe-coverage-specialist", run_in_background: true })
+Task({ prompt: "Security audit",     subagent_type: "qe-security-scanner",    run_in_background: true })
+```
+
+<!-- END ruflo-aqe-reference -->
diff --git a/claude/ruflo-reference.md b/claude/ruflo-reference.md
index a21ac6c0..71320fae 100644
--- a/claude/ruflo-reference.md
+++ b/claude/ruflo-reference.md
@@ -314,6 +314,12 @@ ruflo-setup-aqe --force          # force reinitialize (aqe init --auto --upgrade
 
 Opt-in only — `ruflo-setup-project` does NOT run it.
 
+When agentic-qe **is** installed, the kit also merges a conditional **`ruflo-aqe-reference`**
+block (AQE operating guidance — policies + MCP tool usage + QE-agent patterns) into this same
+`~/.claude/CLAUDE.md`, just below this `ruflo-reference` block. It is added when `aqe` is on
+PATH and **stripped automatically when agentic-qe is absent**. Source: `claude/aqe-reference.md`;
+applied by `install.sh` and re-asserted by `ruflo-reference-refresh` / `ruflo-resync`.
+
 ### Security surface (verify + activate)
 
 ```bash
diff --git a/install.sh b/install.sh
index c8fe4a97..ada4fa99 100755
--- a/install.sh
+++ b/install.sh
@@ -187,11 +187,12 @@ case ":$PATH:" in
 esac
 echo ""
 
-# CLAUDE.md reference template
+# CLAUDE.md reference template (+ the conditional agentic-qe sub-block template)
 echo "## CLAUDE.md reference template -> $CFG_DIR/claude-md-template.md"
 run "mkdir -p '$CFG_DIR'"
 run "cp '$HERE/claude/ruflo-reference.md' '$CFG_DIR/claude-md-template.md'"
-ok "template installed"
+run "cp '$HERE/claude/aqe-reference.md' '$CFG_DIR/aqe-md-template.md'"
+ok "templates installed (ruflo-reference + conditional aqe-reference)"
 echo ""
 
 # Shared helper lib — deployed to a stable absolute path so the standalone bin
@@ -224,6 +225,26 @@ else
 fi
 echo ""
 
+# Conditional agentic-qe operating block: present in ~/.claude/CLAUDE.md ONLY when agentic-qe
+# is installed; stripped otherwise (self-healing on uninstall). Idempotent.
+echo "## ruflo-aqe-reference block (conditional on agentic-qe) -> $CLAUDE_MD"
+AQE_BEGIN='<!-- BEGIN ruflo-aqe-reference -->'; AQE_END='<!-- END ruflo-aqe-reference -->'
+if [ "$DRY" -eq 1 ]; then
+	if have aqe; then printf '%s[dry-run]%s upsert ruflo-aqe-reference block (aqe present)\n' "$C_DIM" "$C_RESET"
+	else printf '%s[dry-run]%s strip ruflo-aqe-reference block (aqe absent)\n' "$C_DIM" "$C_RESET"; fi
+elif have aqe; then
+	_ruflo_block_upsert "$CLAUDE_MD" "$AQE_BEGIN" "$AQE_END" "$HERE/claude/aqe-reference.md" \
+		&& ok "agentic-qe present — merged ruflo-aqe-reference block" \
+		|| warn "could not merge ruflo-aqe-reference block (aqe-reference.md unreadable)"
+else
+	if [ -f "$CLAUDE_MD" ] && grep -qF "$AQE_BEGIN" "$CLAUDE_MD"; then
+		_ruflo_block_strip "$CLAUDE_MD" "$AQE_BEGIN" "$AQE_END"; ok "agentic-qe absent — stripped stale ruflo-aqe-reference block"
+	else
+		dim "agentic-qe absent — no ruflo-aqe-reference block to manage"
+	fi
+fi
+echo ""
+
 # Shell rc source line
 if [ "$EDIT_RC" -eq 1 ]; then
 	echo "## shell functions"
diff --git a/shell/ruflo-functions.sh b/shell/ruflo-functions.sh
index e16ce0e0..0d3f542b 100644
--- a/shell/ruflo-functions.sh
+++ b/shell/ruflo-functions.sh
@@ -651,6 +651,25 @@ ruflo-neural-train() {
 #
 #   ruflo-resync           # re-apply learning + statusline (recommended after upgrade)
 #   ruflo-resync --aqe     # also refresh agentic-qe skills in this repo
+# Sync the conditional agentic-qe sub-block in ~/.claude/CLAUDE.md: present iff `aqe` is
+# installed (upsert from the staged template), stripped otherwise (self-healing on uninstall).
+# Quiet unless the block's presence actually changes. Needs ruflo-lib.sh (_ruflo_block_*).
+_ruflo_sync_aqe_block() {
+	local ref="$HOME/.claude/CLAUDE.md"
+	local tmpl="$HOME/.config/ruflo/aqe-md-template.md"
+	local b='<!-- BEGIN ruflo-aqe-reference -->' e='<!-- END ruflo-aqe-reference -->'
+	command -v _ruflo_block_upsert >/dev/null 2>&1 || return 0
+	[ -f "$ref" ] || return 0
+	if command -v aqe >/dev/null 2>&1; then
+		[ -f "$tmpl" ] || return 0
+		grep -qF "$b" "$ref" || echo "  + agentic-qe present → adding ruflo-aqe-reference block to $ref"
+		_ruflo_block_upsert "$ref" "$b" "$e" "$tmpl"
+	elif grep -qF "$b" "$ref" 2>/dev/null; then
+		echo "  - agentic-qe absent → stripping stale ruflo-aqe-reference block from $ref"
+		_ruflo_block_strip "$ref" "$b" "$e"
+	fi
+}
+
 ruflo-resync() {
 	local do_aqe=0
 	[ "${1:-}" = "--aqe" ] && do_aqe=1
@@ -668,6 +687,9 @@ ruflo-resync() {
 	echo ""; echo "## 3/4 statusline (version + activation footer) for this project"
 	ruflo-fix-statusline-version
 
+	echo ""; echo "## machine-wide ~/.claude/CLAUDE.md: conditional agentic-qe reference block"
+	_ruflo_sync_aqe_block && echo "✓ ruflo-aqe-reference block in sync with agentic-qe install state"
+
 	if [ "$do_aqe" -eq 1 ]; then
 		echo ""; echo "## 4/4 refresh agentic-qe skills (--aqe)"
 		if [ -f .agentic-qe/memory.db ]; then
@@ -697,22 +719,31 @@ ruflo-reference-refresh() {
 		case "$1" in
 			--diff) mode="diff" ;;
 			--regenerate) mode="regenerate" ;;
+			--sync-aqe) mode="sync-aqe" ;;
 			-y|--yes) yes=1 ;;
-			-h|--help) echo "Usage: ruflo-reference-refresh [--diff|--regenerate [-y]]"; return 0 ;;
+			-h|--help) echo "Usage: ruflo-reference-refresh [--diff|--regenerate [-y]|--sync-aqe]"; return 0 ;;
 			*) echo "Unknown flag: $1"; return 2 ;;
 		esac
 		shift
 	done
+	# --sync-aqe only touches the conditional agentic-qe block; no ruflo template needed.
+	if [ "$mode" = "sync-aqe" ]; then _ruflo_sync_aqe_block; return 0; fi
 	if [ ! -f "$template" ]; then
 		echo "No template at $template (run install.sh, or extract from $ref)."
 		return 1
 	fi
+	local aqe_begin='<!-- BEGIN ruflo-aqe-reference -->'
 	case "$mode" in
 		status)
 			echo "ruflo: $(ruflo --version 2>/dev/null || echo 'not installed')"
 			echo "installed sentinel: $(grep -E 'ruflo-version' "$ref" 2>/dev/null || echo 'none')"
 			echo "template  sentinel: $(grep -E 'ruflo-version' "$template" 2>/dev/null || echo 'none')"
-			echo "Use --diff to compare, --regenerate to rebuild."
+			if command -v aqe >/dev/null 2>&1; then
+				grep -qF "$aqe_begin" "$ref" 2>/dev/null && echo "agentic-qe: installed — aqe block present" || echo "agentic-qe: installed — aqe block MISSING (run --sync-aqe)"
+			else
+				grep -qF "$aqe_begin" "$ref" 2>/dev/null && echo "agentic-qe: absent — aqe block STALE (run --sync-aqe to strip)" || echo "agentic-qe: absent — aqe block correctly absent"
+			fi
+			echo "Use --diff to compare, --regenerate to rebuild, --sync-aqe to fix the agentic-qe block."
 			;;
 		diff)
 			local blk; blk=$(mktemp)
@@ -721,13 +752,13 @@ ruflo-reference-refresh() {
 			rm -f "$blk"
 			;;
 		regenerate)
-			if [ ! -f "$ref" ]; then cp "$template" "$ref"; echo "✓ Installed reference at $ref"; return 0; fi
+			if [ ! -f "$ref" ]; then cp "$template" "$ref"; echo "✓ Installed reference at $ref"; _ruflo_sync_aqe_block; return 0; fi
 			local pre post new
 			pre=$(mktemp); post=$(mktemp); new=$(mktemp)
 			awk '/<!-- BEGIN ruflo-reference -->/{exit} {print}' "$ref" > "$pre"
 			awk 'f; /<!-- END ruflo-reference -->/{f=1}' "$ref" > "$post"
 			cat "$pre" "$template" "$post" > "$new"
-			if diff -q "$ref" "$new" >/dev/null 2>&1; then echo "✓ Already up-to-date."; rm -f "$pre" "$post" "$new"; return 0; fi
+			if diff -q "$ref" "$new" >/dev/null 2>&1; then echo "✓ Already up-to-date."; rm -f "$pre" "$post" "$new"; _ruflo_sync_aqe_block; return 0; fi
 			diff -u "$ref" "$new" | head -80
 			if [ "$yes" -eq 0 ]; then
 				printf "Apply this regeneration? [y/N] "; local r; read -r r
@@ -736,6 +767,7 @@ ruflo-reference-refresh() {
 			cp "$ref" "$ref.bak.$(date +%Y%m%d-%H%M%S)"
 			mv "$new" "$ref"; rm -f "$pre" "$post"
 			echo "✓ Regenerated $ref (backup saved)"
+			_ruflo_sync_aqe_block
 			;;
 	esac
 }
diff --git a/shell/ruflo-lib.sh b/shell/ruflo-lib.sh
index 53b56f26..e81f462f 100644
--- a/shell/ruflo-lib.sh
+++ b/shell/ruflo-lib.sh
@@ -99,4 +99,44 @@ _ruflo_bsq3_install() {
 	( cd "$1" && npm install "better-sqlite3@${2:-^12}" --no-save --no-audit --no-fund >/dev/null 2>&1 )
 }
 
+# --- sentinel-delimited block management (CLAUDE.md sub-blocks) -------------
+# Manage a `<!-- BEGIN x -->`…`<!-- END x -->` block in a file. Used for the
+# conditional ruflo-aqe-reference block in ~/.claude/CLAUDE.md (present only when
+# agentic-qe is installed). Idempotent; preserves everything outside the markers.
+# Markers are matched as fixed substrings (awk index()).
+
+# _ruflo_block_upsert FILE BEGIN END SRC — replace the BEGIN..END block in FILE with
+# the contents of SRC (which must itself contain the markers); append if the block is
+# absent; create FILE from SRC if FILE is missing. Returns 1 if SRC is unreadable.
+_ruflo_block_upsert() {
+	local file="$1" begin="$2" end="$3" src="$4"
+	[ -f "$src" ] || return 1
+	mkdir -p "$(dirname "$file")" 2>/dev/null
+	if [ ! -f "$file" ]; then cat "$src" > "$file"; return 0; fi
+	if grep -qF "$begin" "$file"; then
+		local pre post new; pre=$(mktemp); post=$(mktemp); new=$(mktemp)
+		awk -v b="$begin" 'index($0,b){exit} {print}' "$file" > "$pre"
+		awk -v e="$end" 'f; index($0,e){f=1}' "$file" > "$post"
+		cat "$pre" "$src" "$post" > "$new"
+		cat "$new" > "$file"; rm -f "$pre" "$post" "$new"
+	else
+		{ printf '\n'; cat "$src"; } >> "$file"
+	fi
+}
+
+# _ruflo_block_strip FILE BEGIN END — remove the BEGIN..END block (inclusive) from
+# FILE. No-op if FILE or the block is absent.
+_ruflo_block_strip() {
+	local file="$1" begin="$2" end="$3"
+	[ -f "$file" ] || return 0
+	grep -qF "$begin" "$file" || return 0
+	local new; new=$(mktemp)
+	awk -v b="$begin" -v e="$end" '
+		index($0,b){skip=1}
+		!skip{print}
+		index($0,e){skip=0}
+	' "$file" > "$new"
+	cat "$new" > "$file"; rm -f "$new"
+}
+
 _RUFLO_LIB=1   # sentinel: consumers check this to confirm the lib loaded
diff --git a/uninstall.sh b/uninstall.sh
index 7402ed7e..d60f1063 100755
--- a/uninstall.sh
+++ b/uninstall.sh
@@ -4,9 +4,9 @@
 #
 # By default removes ONLY the kit's own footprint:
 #   - every helper this repo ships in bin/ from ~/.local/bin/ (derived from bin/)
-#   - ~/.config/ruflo/claude-md-template.md
-#   - the BEGIN/END ruflo-reference block from ~/.claude/CLAUDE.md (content
-#     outside the sentinels is preserved)
+#   - ~/.config/ruflo/{claude-md-template,aqe-md-template}.md
+#   - the BEGIN/END ruflo-reference AND ruflo-aqe-reference blocks from
+#     ~/.claude/CLAUDE.md (content outside the sentinels is preserved)
 #   - the source line from ~/.zshrc / ~/.bashrc
 #
 # Leaves your ruflo install, memory DBs, and project files untouched. Per-project
@@ -86,23 +86,24 @@ for src in "$HERE"/bin/*; do
 	[ -f "$f" ] && { run "rm -f '$f'"; ok "removed $f"; }
 done
 
-# 2. template
+# 2. templates (ruflo-reference + conditional agentic-qe block)
 [ -f "$HOME/.config/ruflo/claude-md-template.md" ] && { run "rm -f '$HOME/.config/ruflo/claude-md-template.md'"; ok "removed template"; }
+[ -f "$HOME/.config/ruflo/aqe-md-template.md" ] && { run "rm -f '$HOME/.config/ruflo/aqe-md-template.md'"; ok "removed agentic-qe template"; }
 
 # 2b. shared helper lib (already sourced at the top, so removing it here is safe)
 [ -f "$HOME/.config/ruflo/ruflo-lib.sh" ] && { run "rm -f '$HOME/.config/ruflo/ruflo-lib.sh'"; ok "removed helper lib"; }
 
-# 3. CLAUDE.md managed block
+# 3. CLAUDE.md managed blocks (ruflo-reference + the conditional ruflo-aqe-reference)
 CLAUDE_MD="$HOME/.claude/CLAUDE.md"
-if [ -f "$CLAUDE_MD" ] && grep -q '<!-- BEGIN ruflo-reference -->' "$CLAUDE_MD"; then
+if [ -f "$CLAUDE_MD" ] && grep -qE '<!-- BEGIN ruflo-(reference|aqe-reference) -->' "$CLAUDE_MD"; then
 	if [ "$DRY" -eq 1 ]; then
-		printf '%s[dry-run]%s strip ruflo-reference block from %s\n' "$C_DIM" "$C_RESET" "$CLAUDE_MD"
+		printf '%s[dry-run]%s strip ruflo-reference + ruflo-aqe-reference blocks from %s\n' "$C_DIM" "$C_RESET" "$CLAUDE_MD"
 	else
 		cp "$CLAUDE_MD" "$CLAUDE_MD.bak.$(date +%Y%m%d-%H%M%S)"
 		new=$(mktemp)
-		awk '/<!-- BEGIN ruflo-reference -->/{skip=1} /<!-- END ruflo-reference -->/{skip=0; next} !skip' "$CLAUDE_MD" > "$new"
+		awk '/<!-- BEGIN ruflo-reference -->/{skip=1} /<!-- BEGIN ruflo-aqe-reference -->/{skip=1} /<!-- END ruflo-reference -->/{skip=0; next} /<!-- END ruflo-aqe-reference -->/{skip=0; next} !skip' "$CLAUDE_MD" > "$new"
 		mv "$new" "$CLAUDE_MD"
-		ok "stripped ruflo-reference block (backup saved; rest of file preserved)"
+		ok "stripped ruflo-reference + ruflo-aqe-reference blocks (backup saved; rest of file preserved)"
 	fi
 fi