Fix issue #24: listFiles() returns paths relative to cwd, not the listed directory (#105)

* feat: brain-24-1775264868

* chore: remove debug outputs/ artifacts that break go build

The outputs/ directory contained debug Go files with conflicting package
declarations that caused CI build failures. Simplified .gitignore to
exclude the entire outputs/ directory.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: jpleva91

.gitignore

@@ -6,11 +6,7 @@
 dist/
 
 # Agent outputs (generated at runtime)
-outputs/logs/*.log
-outputs/logs/*.md
-outputs/logs/*.jsonl
-outputs/reports/*.md
-outputs/reports/*.jsonl
+outputs/
 
 # Environment
 .env

internal/tools/tools.go

@@ -198,7 +198,8 @@ if err != nil {
 return nil
 }
 name := d.Name()
-if name == "node_modules" || name == ".git" || strings.HasPrefix(name, ".") {
+// Skip hidden files/directories and special directories, but not the root directory
+if path != dir && (name == "node_modules" || name == ".git" || strings.HasPrefix(name, ".")) {
 if d.IsDir() {
 return filepath.SkipDir
 }
@@ -210,7 +211,11 @@ return fmt.Errorf("limit reached")
 if ext != "" && filepath.Ext(name) != ext {
 return nil
 }
-rel, _ := filepath.Rel(".", path)
+rel, _ := filepath.Rel(dir, path)
+// Skip the root directory itself (it will be ".")
+if rel == "." {
+return nil
+}
 if d.IsDir() {
 files = append(files, rel+"/")
 } else {

internal/tools/tools_test.go

@@ -473,3 +473,172 @@ func TestExecuteDirect_Grep(t *testing.T) {
 		t.Fatalf("expected match, got: %s", r.Output)
 	}
 }
+
+// ── list_files tests ──
+
+func TestListFiles_Basic(t *testing.T) {
+	dir := t.TempDir()
+	os.WriteFile(filepath.Join(dir, "a.txt"), []byte(""), 0o644)
+	os.WriteFile(filepath.Join(dir, "b.go"), []byte(""), 0o644)
+	sub := filepath.Join(dir, "sub")
+	os.MkdirAll(sub, 0o755)
+	os.WriteFile(filepath.Join(sub, "c.md"), []byte(""), 0o644)
+
+	// Save original working directory
+	originalWd, _ := os.Getwd()
+	defer os.Chdir(originalWd)
+
+	// Change to a different directory to test relative paths
+	os.Chdir("/tmp")
+
+	r := listFiles(map[string]string{
+		"directory": dir,
+	}, 0)
+
+	if !r.Success {
+		t.Fatalf("expected success, got error: %s", r.Error)
+	}
+
+	// Check that paths are relative to 'dir', not to cwd
+	lines := strings.Split(strings.TrimSpace(r.Output), "\n")
+	expected := []string{"a.txt", "b.go", "sub/", "sub/c.md"}
+	if len(lines) != len(expected) {
+		t.Fatalf("expected %d lines, got %d: %s", len(expected), len(lines), r.Output)
+	}
+
+	for i, line := range lines {
+		if line != expected[i] {
+			t.Errorf("line %d: got %q, want %q", i, line, expected[i])
+		}
+	}
+}
+
+func TestListFiles_FromWithinDirectory(t *testing.T) {
+	dir := t.TempDir()
+	os.WriteFile(filepath.Join(dir, "test.txt"), []byte(""), 0o644)
+
+	// Save original working directory
+	originalWd, _ := os.Getwd()
+	defer os.Chdir(originalWd)
+
+	// Change to the test directory
+	os.Chdir(dir)
+
+	r := listFiles(map[string]string{
+		"directory": ".",
+	}, 0)
+
+	if !r.Success {
+		t.Fatalf("expected success, got error: %s", r.Error)
+	}
+
+	// Should list files relative to current directory (.)
+	lines := strings.Split(strings.TrimSpace(r.Output), "\n")
+	if len(lines) != 1 || lines[0] != "test.txt" {
+		t.Fatalf("expected ['test.txt'], got %v", lines)
+	}
+}
+
+func TestListFiles_ExtensionFilter(t *testing.T) {
+	dir := t.TempDir()
+	os.WriteFile(filepath.Join(dir, "a.txt"), []byte(""), 0o644)
+	os.WriteFile(filepath.Join(dir, "b.go"), []byte(""), 0o644)
+	os.WriteFile(filepath.Join(dir, "c.go"), []byte(""), 0o644)
+
+	r := listFiles(map[string]string{
+		"directory": dir,
+		"extension": ".go",
+	}, 0)
+
+	if !r.Success {
+		t.Fatalf("expected success, got error: %s", r.Error)
+	}
+
+	lines := strings.Split(strings.TrimSpace(r.Output), "\n")
+	if len(lines) != 2 {
+		t.Fatalf("expected 2 .go files, got %d: %s", len(lines), r.Output)
+	}
+	for _, line := range lines {
+		if !strings.HasSuffix(line, ".go") {
+			t.Errorf("expected .go file, got %q", line)
+		}
+	}
+}
+
+func TestListFiles_EmptyDirectory(t *testing.T) {
+	dir := t.TempDir()
+
+	r := listFiles(map[string]string{
+		"directory": dir,
+	}, 0)
+
+	if !r.Success {
+		t.Fatalf("expected success, got error: %s", r.Error)
+	}
+	if r.Output != "(empty directory)" {
+		t.Fatalf("expected '(empty directory)', got %q", r.Output)
+	}
+}
+
+func TestListFiles_SkipsHiddenAndSpecialDirs(t *testing.T) {
+	dir := t.TempDir()
+	os.WriteFile(filepath.Join(dir, "normal.txt"), []byte(""), 0o644)
+	os.WriteFile(filepath.Join(dir, ".hidden"), []byte(""), 0o644)
+	gitDir := filepath.Join(dir, ".git")
+	os.MkdirAll(gitDir, 0o755)
+	os.WriteFile(filepath.Join(gitDir, "config"), []byte(""), 0o644)
+	nodeModules := filepath.Join(dir, "node_modules")
+	os.MkdirAll(nodeModules, 0o755)
+	os.WriteFile(filepath.Join(nodeModules, "package.json"), []byte(""), 0o644)
+
+	r := listFiles(map[string]string{
+		"directory": dir,
+	}, 0)
+
+	if !r.Success {
+		t.Fatalf("expected success, got error: %s", r.Error)
+	}
+
+	// Should only show normal.txt
+	lines := strings.Split(strings.TrimSpace(r.Output), "\n")
+	if len(lines) != 1 || lines[0] != "normal.txt" {
+		t.Fatalf("expected only 'normal.txt', got %v", lines)
+	}
+}
+
+func TestListFiles_SubdirectoryListing(t *testing.T) {
+	dir := t.TempDir()
+	sub := filepath.Join(dir, "subdir")
+	os.MkdirAll(sub, 0o755)
+	os.WriteFile(filepath.Join(sub, "file.txt"), []byte(""), 0o644)
+	os.WriteFile(filepath.Join(sub, "another.md"), []byte(""), 0o644)
+
+	r := listFiles(map[string]string{
+		"directory": sub,
+	}, 0)
+
+	if !r.Success {
+		t.Fatalf("expected success, got error: %s", r.Error)
+	}
+
+	// Should list files relative to subdir
+	lines := strings.Split(strings.TrimSpace(r.Output), "\n")
+	expected := []string{"file.txt", "another.md"}
+	if len(lines) != len(expected) {
+		t.Fatalf("expected %d lines, got %d: %s", len(expected), len(lines), r.Output)
+	}
+	// Check that we have both files (order may vary)
+	hasFileTxt := false
+	hasAnotherMd := false
+	for _, line := range lines {
+		if line == "file.txt" {
+			hasFileTxt = true
+		}
+		if line == "another.md" {
+			hasAnotherMd = true
+		}
+	}
+	if !hasFileTxt || !hasAnotherMd {
+		t.Errorf("missing expected files: got %v", lines)
+	}
+}