diff --git a/README.md b/README.md
index 25dc3b9..b7b952b 100644
--- a/README.md
+++ b/README.md
@@ -11,6 +11,18 @@ brew tap satococoa/tap
 brew install satococoa/tap/git-worktreeinclude
 ```
 
+### Install (Go)
+
+With Go 1.26 or later installed:
+
+```sh
+go install github.com/satococoa/git-worktreeinclude/cmd/git-worktreeinclude@latest
+```
+
+Add your Go binary installation directory (`GOBIN`, or `$(go env GOPATH)/bin` when `GOBIN` is unset) to `PATH`. This also enables `git worktreeinclude apply`.
+
+Builds installed with `go install` currently report `dev` for `--version`; the installed module version can be inspected with `go version -m` on the binary.
+
 ### Build
 
 ```sh
@@ -42,7 +54,7 @@ git worktreeinclude apply
   - Paths matching `.worktreeinclude`
   - Paths Git classifies as ignored
 
-Tracked files are never copied, even if listed in `.worktreeinclude`.
+Files tracked in either the source or target worktree are never copied, even if listed in `.worktreeinclude`, missing from the target working tree, or used with `--force`.
 
 Example for a typical app repo with local env, editor settings, and tool-specific cache:
 
diff --git a/internal/cli/cli.go b/internal/cli/cli.go
index 2ad82ab..f3e0d7b 100644
--- a/internal/cli/cli.go
+++ b/internal/cli/cli.go
@@ -243,7 +243,7 @@ func formatActionLine(action engine.Action, force bool) string {
 		return fmt.Sprintf("COPY      %s", action.Path)
 	case "conflict":
 		if force {
-			return fmt.Sprintf("COPY      %s", action.Path)
+			return fmt.Sprintf("CONFLICT  %s (unresolved by --force)", action.Path)
 		}
 		return fmt.Sprintf("CONFLICT  %s (differs; use --force)", action.Path)
 	case "skip":
diff --git a/internal/cli/directory_conflict_integration_test.go b/internal/cli/directory_conflict_integration_test.go
new file mode 100644
index 0000000..a3e53a9
--- /dev/null
+++ b/internal/cli/directory_conflict_integration_test.go
@@ -0,0 +1,85 @@
+package cli_test
+
+import (
+	"fmt"
+	"os"
+	"path/filepath"
+	"strings"
+	"testing"
+)
+
+func TestApplyDirectoryConflictRemainsAnError(t *testing.T) {
+	for _, force := range []bool{false, true} {
+		for _, dryRun := range []bool{false, true} {
+			for _, jsonOutput := range []bool{false, true} {
+				t.Run(fmt.Sprintf("force=%t/dry=%t/json=%t", force, dryRun, jsonOutput), func(t *testing.T) {
+					fx := setupFixture(t)
+					writeFile(t, filepath.Join(fx.root, testIncludeFile), ".env\n.env.local\n")
+					target := filepath.Join(fx.wt, ".env")
+					if err := os.Mkdir(target, 0o755); err != nil {
+						t.Fatal(err)
+					}
+					child := filepath.Join(target, "keep")
+					writeFile(t, child, "KEEP\n")
+					args := []string{"apply", "--include", testIncludeFile}
+					if force {
+						args = append(args, "--force")
+					}
+					if dryRun {
+						args = append(args, "--dry-run")
+					}
+					if jsonOutput {
+						args = append(args, "--json")
+					}
+					stdout, stderr, code := runCmd(t, fx.wt, nil, testBinary, args...)
+					if code != 3 || strings.TrimSpace(stderr) != "" {
+						t.Fatalf("code=%d stderr=%q stdout=%q", code, stderr, stdout)
+					}
+					data, err := os.ReadFile(child)
+					if err != nil || string(data) != "KEEP\n" {
+						t.Fatalf("directory contents changed: %q, %v", data, err)
+					}
+					other := filepath.Join(fx.wt, ".env.local")
+					if dryRun {
+						if _, err := os.Lstat(other); !os.IsNotExist(err) {
+							t.Fatalf("dry-run wrote other file: %v", err)
+						}
+					} else {
+						data, err := os.ReadFile(other)
+						if err != nil || string(data) != "SOURCE_LOCAL\n" {
+							t.Fatalf("non-conflicting file not copied: %q, %v", data, err)
+						}
+					}
+					if jsonOutput {
+						res := decodeSingleJSON(t, stdout)
+						if res.DryRun != dryRun || res.Summary.Conflicts != 1 || res.Summary.Errors != 0 || len(res.Actions) != 2 {
+							t.Fatalf("incorrect conflict result: %+v", res)
+						}
+						if dryRun && (res.Summary.CopyPlanned != 1 || res.Summary.Copied != 0) || !dryRun && res.Summary.Copied != 1 {
+							t.Fatalf("incorrect copy summary: %+v", res.Summary)
+						}
+						found := false
+						for _, action := range res.Actions {
+							if action.Path == ".env" {
+								found = true
+								if action.Op != "conflict" || action.Status != "diff" {
+									t.Fatalf("incorrect directory action: %+v", action)
+								}
+							}
+						}
+						if !found {
+							t.Fatal("directory conflict action missing")
+						}
+					} else {
+						if !strings.Contains(stdout, "CONFLICT  .env (") || strings.Contains(stdout, "COPY      .env\n") {
+							t.Fatalf("directory must be reported as conflict, not copied: %q", stdout)
+						}
+						if force && strings.Contains(stdout, "use --force") {
+							t.Fatalf("force cannot resolve this conflict: %q", stdout)
+						}
+					}
+				})
+			}
+		}
+	}
+}
diff --git a/internal/cli/tracked_integration_test.go b/internal/cli/tracked_integration_test.go
new file mode 100644
index 0000000..46afdf5
--- /dev/null
+++ b/internal/cli/tracked_integration_test.go
@@ -0,0 +1,73 @@
+package cli_test
+
+import (
+	"fmt"
+	"os"
+	"path/filepath"
+	"strings"
+	"testing"
+)
+
+func TestApplyProtectsTrackedFilesInEitherWorktree(t *testing.T) {
+	for _, tracking := range []struct {
+		name           string
+		source, target bool
+	}{
+		{"source", true, false},
+		{"target", false, true},
+		{"both", true, true},
+	} {
+		for _, deleted := range []bool{false, true} {
+			for _, force := range []bool{false, true} {
+				for _, dryRun := range []bool{false, true} {
+					t.Run(fmt.Sprintf("%s/deleted=%t/force=%t/dry=%t", tracking.name, deleted, force, dryRun), func(t *testing.T) {
+						fx := setupFixture(t)
+						writeFile(t, filepath.Join(fx.root, testIncludeFile), ".env\n")
+						target := filepath.Join(fx.wt, ".env")
+						writeFile(t, target, "TARGET\n")
+						if tracking.source {
+							runGit(t, fx.root, "add", "-f", ".env")
+						}
+						if tracking.target {
+							runGit(t, fx.wt, "add", "-f", ".env")
+						}
+						if deleted {
+							if err := os.Remove(target); err != nil {
+								t.Fatal(err)
+							}
+						}
+						before := runGit(t, fx.wt, "status", "--porcelain=v1", "--untracked-files=all")
+						args := []string{"apply", "--include", testIncludeFile, "--json"}
+						if force {
+							args = append(args, "--force")
+						}
+						if dryRun {
+							args = append(args, "--dry-run")
+						}
+						stdout, stderr, code := runCmd(t, fx.wt, nil, testBinary, args...)
+						if code != 0 || strings.TrimSpace(stderr) != "" {
+							t.Fatalf("code=%d stderr=%q", code, stderr)
+						}
+						res := decodeSingleJSON(t, stdout)
+						if res.DryRun != dryRun || res.Summary.Matched != 0 || len(res.Actions) != 0 {
+							t.Fatalf("tracked files must not be planned or copied: %+v", res)
+						}
+						if deleted {
+							if _, err := os.Lstat(target); !os.IsNotExist(err) {
+								t.Fatalf("deleted file was restored: %v", err)
+							}
+						} else {
+							data, err := os.ReadFile(target)
+							if err != nil || string(data) != "TARGET\n" {
+								t.Fatalf("target changed: %q, %v", data, err)
+							}
+						}
+						if after := runGit(t, fx.wt, "status", "--porcelain=v1", "--untracked-files=all"); after != before {
+							t.Fatalf("target status changed: before=%q after=%q", before, after)
+						}
+					})
+				}
+			}
+		}
+	}
+}
diff --git a/internal/engine/engine.go b/internal/engine/engine.go
index 4a5f895..210dc6d 100644
--- a/internal/engine/engine.go
+++ b/internal/engine/engine.go
@@ -256,7 +256,7 @@ func (e *Engine) executePrepared(prep prepared, dryRun, force bool) (Result, int
 	if result.Summary.Errors > 0 {
 		return result, exitcode.Internal
 	}
-	if result.Summary.Conflicts > 0 && !force {
+	if result.Summary.Conflicts > 0 {
 		return result, exitcode.Conflict
 	}
 	return result, exitcode.OK
@@ -342,6 +342,28 @@ func (e *Engine) prepare(ctx context.Context, cwd, fromOpt, includeOpt string) (
 		return prepared{}, err
 	}
 	prep.matched = intersectPaths(ignored, included)
+
+	// The source and target have separate indexes. A source-ignored path may
+	// still be tracked in the target, even when its working-tree file is absent.
+	trackedOutput, err := e.git.Run(ctx, targetRoot, "ls-files", "--cached", "-z")
+	if err != nil {
+		return prepared{}, &CLIError{Code: exitcode.Env, Msg: "failed to list target tracked files", Err: err}
+	}
+	tracked, err := parseNULPaths(trackedOutput)
+	if err != nil {
+		return prepared{}, &CLIError{Code: exitcode.Env, Msg: "failed to parse target tracked files", Err: err}
+	}
+	trackedSet := make(map[string]struct{}, len(tracked))
+	for _, rel := range tracked {
+		trackedSet[rel] = struct{}{}
+	}
+	matched := prep.matched[:0]
+	for _, rel := range prep.matched {
+		if _, isTracked := trackedSet[rel]; !isTracked {
+			matched = append(matched, rel)
+		}
+	}
+	prep.matched = matched
 	return prep, nil
 }