diff --git a/scripts/smoke-test.sh b/scripts/smoke-test.sh
index 477cc6ab3..7887c3146 100755
--- a/scripts/smoke-test.sh
+++ b/scripts/smoke-test.sh
@@ -116,6 +116,16 @@ copy_smoke_binary() {
   cp "$BINARY" "$destination"
 }
 
+# A fixture home that belongs to a Claude Code user. An empty ~/.claude is not
+# evidence of one (#1180: other tools create that directory, and install then
+# configured a client the user never had); the user config Claude Code itself
+# writes is. Same seed as test_mark_claude_code_installed in tests/test_cli.c.
+mark_claude_code_installed() {
+  local home="$1"
+  mkdir -p "$home/.claude"
+  echo '{}' > "$home/.claude.json"
+}
+
 # Retire this run's private account daemon (if one is running) and wait until
 # it reports not-running. Install/uninstall flows leave an ephemeral daemon
 # draining asynchronously whose mapped generation backing and open logs
@@ -2149,10 +2159,10 @@ if ! grep -q '^name: codebase-memory$' "$HERMES_HOME_DIR/skills/codebase-memory/
   exit 1
 fi
 echo "OK 8x-i: Hermes durable delegation skill"
-if ! grep -q '^hooks:' "$FAKE_HOME/.hermes/config.yaml" 2>/dev/null ||
-   ! grep -q '^  pre_llm_call:' "$FAKE_HOME/.hermes/config.yaml" 2>/dev/null ||
-   ! grep -q 'hook-augment' "$FAKE_HOME/.hermes/config.yaml" 2>/dev/null ||
-   ! grep -q -- '--dialect hermes' "$FAKE_HOME/.hermes/config.yaml" 2>/dev/null; then
+if ! grep -q '^hooks:' "$HERMES_HOME_DIR/config.yaml" 2>/dev/null ||
+   ! grep -q '^  pre_llm_call:' "$HERMES_HOME_DIR/config.yaml" 2>/dev/null ||
+   ! grep -q 'hook-augment' "$HERMES_HOME_DIR/config.yaml" 2>/dev/null ||
+   ! grep -q -- '--dialect hermes' "$HERMES_HOME_DIR/config.yaml" 2>/dev/null; then
   echo "FAIL 8x-ii: Hermes pre_llm_call context hook missing"
   exit 1
 fi
@@ -3154,8 +3164,8 @@ fi
 echo "OK 9l: JSON agents, lifecycle hooks, and Kilo cleaned; foreign settings preserved"
 
 # 9m: YAML/TOML new agents are cleaned.
-if grep -q '^  codebase-memory-mcp:' "$FAKE_HOME/.hermes/config.yaml" 2>/dev/null ||
-   grep -q '^  pre_llm_call:' "$FAKE_HOME/.hermes/config.yaml" 2>/dev/null ||
+if grep -q '^  codebase-memory-mcp:' "$HERMES_HOME_DIR/config.yaml" 2>/dev/null ||
+   grep -q '^  pre_llm_call:' "$HERMES_HOME_DIR/config.yaml" 2>/dev/null ||
    grep -q '^  codebase-memory-mcp:' "$GOOSE_CFG" 2>/dev/null ||
    grep -q 'codebase-memory-mcp' "$FAKE_HOME/.grok/config.toml" 2>/dev/null ||
    grep -q '^name = "codebase-memory-mcp"' "$FAKE_HOME/.vibe/config.toml" 2>/dev/null; then
@@ -3209,7 +3219,7 @@ echo "OK 9m-i: durable instruction blocks removed"
 
 # 9n: Skills removed (consolidated skill dir)
 if [ -d "$FAKE_HOME/.claude/skills/codebase-memory" ] ||
-   [ -d "$FAKE_HOME/.hermes/skills/codebase-memory" ] ||
+   [ -d "$HERMES_HOME_DIR/skills/codebase-memory" ] ||
    [ -d "$FAKE_HOME/.agents/skills/codebase-memory" ] ||
    [ -d "$FAKE_HOME/.qoder/skills/codebase-memory" ] ||
    [ -d "$CUSTOM_KIMI_HOME/skills/codebase-memory" ] ||
@@ -3287,9 +3297,40 @@ echo "OK 9b-1: install with minimal agents exits cleanly"
 retire_account_daemon "9b-1-cleanup"
 smoke_rmtree "$EMPTY_HOME"
 
+# 9b-1b (#1180): an empty ~/.claude directory is not a Claude Code install.
+# The empty home above is this venue's control: where it showed no Claude Code,
+# the same home plus a bare ~/.claude must not be configured for it either.
+#
+# SKIP_WHITELIST: a venue with a claude executable (a developer machine) detects
+# Claude Code in every home, so there is nothing for the bare directory to
+# change. Narrowing PATH for this one install does not make such a venue
+# claude-free: with HOME as the scanned home the product also probes fixed
+# locations (/usr/local/bin, /opt/homebrew/bin). A venue without one, such as
+# the Linux test image, runs the check.
+if grep -q 'Detected agents:.* Claude-Code' <<<"$INSTALL_OUT"; then
+  echo "SKIP 9b-1b: a claude executable is installed in this venue (whitelisted above)"
+else
+  BARE_HOME=$(smoke_mktemp_dir)
+  mkdir -p "$BARE_HOME/.claude" "$BARE_HOME/.local/bin"
+  BARE_RC=0
+  BARE_OUT=$(HOME="$BARE_HOME" LOCALAPPDATA="$BARE_HOME/AppData/Local" "$BINARY" install -y 2>&1) || BARE_RC=$?
+  if [ "$BARE_RC" -ge 128 ] ||
+     ! grep -q 'Detected agents:' <<<"$BARE_OUT" ||
+     grep -q 'Detected agents:.* Claude-Code' <<<"$BARE_OUT" ||
+     [ -e "$BARE_HOME/.claude.json" ] ||
+     [ -n "$(ls -A "$BARE_HOME/.claude" 2>/dev/null)" ]; then
+    echo "FAIL 9b-1b: a bare ~/.claude directory was configured as a Claude Code install"
+    exit 1
+  fi
+  echo "OK 9b-1b: a bare ~/.claude directory is not configured as Claude Code"
+  retire_account_daemon "9b-1b-cleanup"
+  smoke_rmtree "$BARE_HOME"
+fi
+
 # 9b-2: Install twice (idempotent)
 IDEM_HOME=$(smoke_mktemp_dir)
-mkdir -p "$IDEM_HOME/.claude" "$IDEM_HOME/.local/bin"
+mkdir -p "$IDEM_HOME/.local/bin"
+mark_claude_code_installed "$IDEM_HOME"
 copy_smoke_binary "$IDEM_HOME/.local/bin/codebase-memory-mcp"
 run_no_crash 9b-2 env HOME="$IDEM_HOME" LOCALAPPDATA="$IDEM_HOME/AppData/Local" "$BINARY" install -y
 IDEM_INSTALLER="$BINARY"
@@ -3313,7 +3354,8 @@ smoke_rmtree "$IDEM_HOME"
 
 # 9b-3: Uninstall without prior install
 CLEAN_HOME=$(smoke_mktemp_dir)
-mkdir -p "$CLEAN_HOME/.claude" "$CLEAN_HOME/.local/bin"
+mkdir -p "$CLEAN_HOME/.local/bin"
+mark_claude_code_installed "$CLEAN_HOME"
 UNINSTALL_RC=0
 UNINSTALL_OUT=$(HOME="$CLEAN_HOME" "$BINARY" uninstall -y -n 2>&1) || UNINSTALL_RC=$?
 if [ "$UNINSTALL_RC" -ge 128 ]; then
@@ -3337,7 +3379,8 @@ smoke_rmtree "$CORRUPT_HOME"
 
 # 9b-8: Double uninstall
 DBL_HOME=$(smoke_mktemp_dir)
-mkdir -p "$DBL_HOME/.claude" "$DBL_HOME/.local/bin"
+mkdir -p "$DBL_HOME/.local/bin"
+mark_claude_code_installed "$DBL_HOME"
 copy_smoke_binary "$DBL_HOME/.local/bin/codebase-memory-mcp"
 run_no_crash 9b-8-install env HOME="$DBL_HOME" "$BINARY" install -y
 DBL_UNINSTALLER="$BINARY"
@@ -3834,7 +3877,7 @@ if [ "$DL_OS" != "windows" ] && [ -f "$REPO_ROOT/install.sh" ]; then
   echo "--- Phase 13: install.sh E2E ---"
   INSTALL_TEST_HOME=$(smoke_mktemp_dir)
   INSTALL_TEST_DIR=$(smoke_mktemp_dir)
-  mkdir -p "$INSTALL_TEST_HOME/.claude"
+  mark_claude_code_installed "$INSTALL_TEST_HOME"
   mkdir -p "$INSTALL_TEST_HOME/.local/bin"
 
   # 13a: run install.sh with local URL + isolated HOME
@@ -3871,7 +3914,8 @@ if [ "$DL_OS" != "windows" ] && [ -f "$REPO_ROOT/install.sh" ]; then
     echo "OK 13d: no signing needed ($DL_OS)"
   fi
 
-  # 13e: agent configs created (at least Claude Code since we made ~/.claude)
+  # 13e: agent configs created (at least Claude Code: the fixture home is a
+  # Claude Code user's)
   if [ -f "$INSTALL_TEST_HOME/.claude.json" ] && grep -q 'codebase-memory-mcp' "$INSTALL_TEST_HOME/.claude.json" 2>/dev/null; then
     echo "OK 13e: agent configs created by install.sh"
   else
@@ -3898,7 +3942,7 @@ elif [ -f "$REPO_ROOT/install.ps1" ] && command -v powershell.exe &>/dev/null; t
   echo "--- Phase 13: install.ps1 E2E (Windows) ---"
   PS1_TEST_HOME=$(smoke_mktemp_dir)
   PS1_TEST_DIR=$(smoke_mktemp_dir)
-  mkdir -p "$PS1_TEST_HOME/.claude"
+  mark_claude_code_installed "$PS1_TEST_HOME"
 
   # Convert MSYS paths to Windows paths for PowerShell
   if command -v cygpath &>/dev/null; then