diff --git a/scripts/install.sh b/scripts/install.sh
index 4e1b9103..2f8e9a91 100755
--- a/scripts/install.sh
+++ b/scripts/install.sh
@@ -314,7 +314,20 @@ resolve_dest() {
     hermes)      var="HERMES_PLUGIN_DIR" ;;
     vibe)        var="VIBE_HOME" ;;
   esac
-  if [[ -n "$var" && -n "${!var:-}" ]]; then printf '%s' "${!var}"; else printf '%s' "$def"; fi
+  if [[ -n "$var" && -n "${!var:-}" ]]; then
+    if [[ "$tool" == "claude-code" ]]; then
+      # CLAUDE_CONFIG_DIR is the config root (it replaces ~/.claude);
+      # agents live in its agents/ subdirectory (fixes #578). Strip one
+      # trailing slash; a value already ending in /agents is used verbatim
+      # so users who worked around the old bug are not double-nested.
+      local cfg="${!var}"; cfg="${cfg%/}"
+      if [[ "$cfg" == */agents ]]; then printf '%s' "$cfg"; else printf '%s' "$cfg/agents"; fi
+    else
+      printf '%s' "${!var}"
+    fi
+  else
+    printf '%s' "$def"
+  fi
 }
 
 # resolve_tool_path <tool> — best-effort binary path for the detection UI.
@@ -415,7 +428,7 @@ check_integrations() {
 # ---------------------------------------------------------------------------
 # Tool detection
 # ---------------------------------------------------------------------------
-detect_claude_code() { [[ -d "${HOME}/.claude" ]]; }
+detect_claude_code() { [[ -d "${CLAUDE_CONFIG_DIR:-${HOME}/.claude}" ]]; }
 detect_copilot()      { command -v code >/dev/null 2>&1 || [[ -d "${HOME}/.github" || -d "${HOME}/.copilot" ]]; }
 detect_antigravity()  { [[ -d "${HOME}/.gemini/config/skills" ]]; }
 detect_gemini_cli()   { command -v gemini >/dev/null 2>&1 || [[ -d "${HOME}/.gemini" ]]; }
diff --git a/scripts/test-install.sh b/scripts/test-install.sh
index 01a14611..f161e6cf 100755
--- a/scripts/test-install.sh
+++ b/scripts/test-install.sh
@@ -186,6 +186,37 @@ RUN_OUT="$(HOME="$home" COPILOT_AGENT_DIR="$home/from-env" "$INSTALL" --no-inter
 assert_eq "$TOTAL_AGENTS" "$(count_md "$home/from-flag")" "--path wins over the env var"
 assert_eq 0 "$(count_md "$home/from-env")" "env var destination is unused when --path is given"
 
+# ---------------------------------------------------------------------------
+# 3b. CLAUDE_CONFIG_DIR is the config root, not the agents dir (issue #578)
+#
+# Claude Code replaces ~/.claude with $CLAUDE_CONFIG_DIR, so agents belong in
+# $CLAUDE_CONFIG_DIR/agents — matching the default ${HOME}/.claude/agents.
+# Before the fix, resolve_dest returned the variable verbatim and agents
+# landed in the config root where Claude Code never loads them; detection
+# also missed relocated configs entirely.
+# ---------------------------------------------------------------------------
+home="$(sandbox claude-config-dir)"
+cfg="$home/.config/claude-code"
+RUN_OUT="$(HOME="$home" CLAUDE_CONFIG_DIR="$cfg" "$INSTALL" --no-interactive --tool claude-code 2>&1)"; RUN_STATUS=$?
+assert_eq 0 "$RUN_STATUS" "CLAUDE_CONFIG_DIR install exits 0"
+assert_eq "$TOTAL_AGENTS" "$(count_md "$cfg/agents")" "CLAUDE_CONFIG_DIR installs agents into \$CLAUDE_CONFIG_DIR/agents"
+assert_eq 0 "$(count_md "$cfg")" "CLAUDE_CONFIG_DIR leaves the config root itself empty"
+
+# Trailing slash and a pre-existing /agents suffix both resolve cleanly.
+home="$(sandbox claude-config-dir-slash)"
+cfg="$home/.config/claude-code/"
+RUN_OUT="$(HOME="$home" CLAUDE_CONFIG_DIR="$cfg" "$INSTALL" --no-interactive --tool claude-code 2>&1)"; RUN_STATUS=$?
+assert_eq 0 "$RUN_STATUS" "trailing-slash CLAUDE_CONFIG_DIR install exits 0"
+assert_eq "$TOTAL_AGENTS" "$(count_md "$home/.config/claude-code/agents")" \
+  "a trailing slash on CLAUDE_CONFIG_DIR still resolves to .../agents"
+
+home="$(sandbox claude-config-dir-agents)"
+cfg="$home/.config/claude-code/agents"
+RUN_OUT="$(HOME="$home" CLAUDE_CONFIG_DIR="$cfg" "$INSTALL" --no-interactive --tool claude-code 2>&1)"; RUN_STATUS=$?
+assert_eq 0 "$RUN_STATUS" "pre-suffixed CLAUDE_CONFIG_DIR install exits 0"
+assert_eq "$TOTAL_AGENTS" "$(count_md "$cfg")" \
+  "a CLAUDE_CONFIG_DIR already ending in /agents is used verbatim (no double-nesting)"
+
 # ---------------------------------------------------------------------------
 # 4. Paths with spaces (regression: word-splitting in the install loop)
 # ---------------------------------------------------------------------------