diff --git a/cmd/dotagents/config.go b/cmd/dotagents/config.go
index 41525df..8368c5d 100644
--- a/cmd/dotagents/config.go
+++ b/cmd/dotagents/config.go
@@ -21,6 +21,9 @@ func loadContext(opts runOptions) (string, string, config, []agentConfig, error)
 		return "", "", config{}, nil, err
 	}
 	repoRoot := filepath.Dir(configPath)
+	if err := refuseWorktreeRoot(repoRoot); err != nil {
+		return "", "", config{}, nil, err
+	}
 
 	cfg, err := loadConfig(repoRoot, home, configPath)
 	if err != nil {
@@ -358,6 +361,34 @@ func absoluteExpandedPath(path string, home string) (string, error) {
 	return abs, nil
 }
 
+// refuseWorktreeRoot rejects repo roots that are (or live under) a linked
+// git worktree. sync materializes absolute links into the repo root; when
+// the worktree is removed those links dangle and every managed skill
+// breaks (ENOENT). The canonical checkout is the only valid root.
+//
+// Two detections: a linked worktree has a .git FILE pointing at its git
+// dir (the canonical checkout has a .git directory or none), and the
+// project convention places worktrees under .worktrees/, which catches
+// roots whose .git check cannot run (missing dir, odd layouts).
+func refuseWorktreeRoot(repoRoot string) error {
+	resolved := repoRoot
+	if real, err := filepath.EvalSymlinks(repoRoot); err == nil {
+		resolved = real
+	}
+	refuse := func() error {
+		return fmt.Errorf("refusing to run with repo root %s: it is (or lives inside) a linked git worktree; materialized links would dangle when the worktree is removed — run from the canonical checkout", repoRoot)
+	}
+	if fi, err := os.Stat(filepath.Join(resolved, ".git")); err == nil && fi.Mode().IsRegular() {
+		return refuse()
+	}
+	for _, seg := range strings.Split(filepath.ToSlash(resolved), "/") {
+		if seg == ".worktrees" {
+			return refuse()
+		}
+	}
+	return nil
+}
+
 func expandPath(path string, home string) string {
 	path = strings.TrimSpace(path)
 	switch {
diff --git a/cmd/dotagents/config_worktree_test.go b/cmd/dotagents/config_worktree_test.go
new file mode 100644
index 0000000..2b1376a
--- /dev/null
+++ b/cmd/dotagents/config_worktree_test.go
@@ -0,0 +1,55 @@
+package main
+
+import (
+	"os"
+	"path/filepath"
+	"strings"
+	"testing"
+)
+
+func TestRefuseWorktreeRoot(t *testing.T) {
+	repo := t.TempDir()
+	if err := refuseWorktreeRoot(repo); err != nil {
+		t.Fatalf("canonical root must be accepted: %v", err)
+	}
+
+	worktree := filepath.Join(repo, ".worktrees", "sync-main")
+	if err := os.MkdirAll(worktree, 0o755); err != nil {
+		t.Fatal(err)
+	}
+	if err := refuseWorktreeRoot(worktree); err == nil {
+		t.Fatal("worktree root must be refused")
+	} else if !strings.Contains(err.Error(), "canonical checkout") {
+		t.Fatalf("unexpected error: %v", err)
+	}
+
+	// A linked worktree outside .worktrees/ is caught by its .git file.
+	arbitrary := filepath.Join(t.TempDir(), "agents-test")
+	if err := os.MkdirAll(arbitrary, 0o755); err != nil {
+		t.Fatal(err)
+	}
+	if err := os.WriteFile(filepath.Join(arbitrary, ".git"), []byte("gitdir: elsewhere\n"), 0o644); err != nil {
+		t.Fatal(err)
+	}
+	if err := refuseWorktreeRoot(arbitrary); err == nil {
+		t.Fatal("linked worktree via .git file must be refused")
+	}
+
+	// A canonical checkout has a .git directory, which is allowed.
+	canonical := filepath.Join(t.TempDir(), "repo")
+	if err := os.MkdirAll(filepath.Join(canonical, ".git"), 0o755); err != nil {
+		t.Fatal(err)
+	}
+	if err := refuseWorktreeRoot(canonical); err != nil {
+		t.Fatalf("canonical checkout with .git dir must be accepted: %v", err)
+	}
+
+	// A symlink aliasing a worktree root resolves to the same refusal.
+	alias := filepath.Join(t.TempDir(), "alias")
+	if err := os.Symlink(worktree, alias); err != nil {
+		t.Skipf("symlink unavailable: %v", err)
+	}
+	if err := refuseWorktreeRoot(alias); err == nil {
+		t.Fatal("symlinked worktree root must be refused")
+	}
+}
diff --git a/cmd/dotagents/setup.go b/cmd/dotagents/setup.go
index 511029d..e43322b 100644
--- a/cmd/dotagents/setup.go
+++ b/cmd/dotagents/setup.go
@@ -22,6 +22,9 @@ func runSetup(opts runOptions) error {
 		return err
 	}
 	repoRoot := filepath.Dir(configPath)
+	if err := refuseWorktreeRoot(repoRoot); err != nil {
+		return err
+	}
 	streams := setupStreams(opts)
 
 	cfg, err := loadSetupConfig(configPath, home)