fix(workspace): discover worktrees nested in boundary dirs

pkg/filesystem/resolve.go

@@ -196,6 +196,11 @@ func discoveryBoundary(cfg *config.Config) func(string) bool {
 		if _, registered := cfg.NameForWorkspacePath(root); registered {
 			return false
 		}
+		// A linked worktree is a working copy of the user's own repo, not a dependency, wherever
+		// a tool chose to put it (Claude Code, for one, nests them under .claude/worktrees).
+		if isLinkedWorktree(root) {
+			return false
+		}
 		parent, found := cfg.WorkspaceForPath(root)
 		if !found {
 			return false
@@ -213,6 +218,26 @@ func discoveryBoundary(cfg *config.Config) func(string) bool {
 	}
 }
 
+// isLinkedWorktree reports whether dir is the root of a `git worktree add` checkout. Its .git is
+// a file pointing at a gitdir that holds a commondir file; a submodule also has a .git file, but
+// its gitdir has no commondir, so a vendored submodule stays behind the boundary.
+func isLinkedWorktree(dir string) bool {
+	data, err := os.ReadFile(filepath.Clean(filepath.Join(dir, ".git")))
+	if err != nil {
+		return false
+	}
+	gitDir, ok := strings.CutPrefix(strings.TrimSpace(string(data)), "gitdir:")
+	if !ok {
+		return false
+	}
+	gitDir = strings.TrimSpace(gitDir)
+	if !filepath.IsAbs(gitDir) {
+		gitDir = filepath.Join(dir, gitDir)
+	}
+	info, err := os.Stat(filepath.Join(gitDir, "commondir"))
+	return err == nil && !info.IsDir()
+}
+
 // loadResolved builds a result for a registered workspace, creating its flow.yaml if the user
 // registered a path that does not have one yet.
 func loadResolved(name, path string, src WorkspaceSource) (*ResolvedWorkspace, error) {

pkg/filesystem/resolve_test.go

@@ -107,6 +107,33 @@ var _ = Describe("ResolveWorkspace", func() {
 			Expect(res.Path).To(Equal(parent))
 		})
 
+		It("discovers a linked worktree nested under a boundary directory", func() {
+			parent := mkWorkspace("repo")
+			worktree := mkWorkspace("repo/.claude/worktrees/feature")
+			gitDir := mkDir("repo/.git/worktrees/feature")
+			Expect(os.WriteFile(filepath.Join(gitDir, "commondir"), []byte("../..\n"), 0600)).To(Succeed())
+			Expect(os.WriteFile(filepath.Join(worktree, ".git"), []byte("gitdir: "+gitDir+"\n"), 0600)).To(Succeed())
+			cfg := dynamic(map[string]string{"repo": parent}, "repo")
+			res, err := filesystem.ResolveWorkspace(cfg, filesystem.ResolveOptions{
+				Dir: mkDir("repo/.claude/worktrees/feature/cmd"),
+			})
+			Expect(err).NotTo(HaveOccurred())
+			Expect(res.Path).To(Equal(worktree))
+			Expect(res.Registered).To(BeFalse())
+			Expect(res.Source).To(Equal(filesystem.SourceDiscovered))
+		})
+
+		It("walks past a vendored submodule inside a registered workspace", func() {
+			parent := mkWorkspace("repo")
+			sub := mkWorkspace("repo/vendor/dep")
+			mkDir("repo/.git/modules/dep")
+			Expect(os.WriteFile(filepath.Join(sub, ".git"), []byte("gitdir: ../../.git/modules/dep\n"), 0600)).To(Succeed())
+			cfg := dynamic(map[string]string{"repo": parent}, "repo")
+			res, err := filesystem.ResolveWorkspace(cfg, filesystem.ResolveOptions{Dir: sub})
+			Expect(err).NotTo(HaveOccurred())
+			Expect(res.Path).To(Equal(parent))
+		})
+
 		It("still discovers a standalone clone under a directory named external", func() {
 			// The boundary only applies inside a registered workspace; an unrelated path that
 			// happens to contain "external" is a legitimate root.