fix: incorrect files when filter conflicts with gitignore

internal/traverse.go

@@ -21,15 +21,16 @@ type PathInfo struct {
 
 // TraverseDirectory traverses the directory and collects path information using the filter package
 func TraverseDirectory(dir string, filterPatterns, gitignorePaths []string) ([]PathInfo, error) {
-	// Create the filter from filter patterns and negated gitignore file patterns.
+	// Create the filter from filter patterns.
 	f := filter.CompileFilterPatterns(filterPatterns...)
+	// Create the gitignore filter from gitignore file paths.
+	gi := new(filter.Filter)
 	for _, giPath := range gitignorePaths {
-		giFilter, err := filter.CompileFilterPatternFile(giPath)
+		tempFilter, err := filter.CompileFilterPatternFile(giPath)
 		if err != nil {
 			return nil, fmt.Errorf("compiling patterns from gitignore file %q: %w", giPath, err)
 		}
-		giFilter.NegateAll()
-		f.Merge(giFilter)
+		gi.MergeWithPrecedence(tempFilter)
 	}
 
 	paths := make([]PathInfo, 0)
@@ -72,24 +73,24 @@ func TraverseDirectory(dir string, filterPatterns, gitignorePaths []string) ([]P
 		if err != nil {
 			return fmt.Errorf("getting relative path between %q and %q: %w", basePath, path, err)
 		}
-
-		// Convert to forward slashes for consistent pattern matching
 		relPath = filepath.ToSlash(relPath)
 
-		// Check if a file path should be included based on patterns
-		if f.MatchesPath(relPath) {
-			relPath, err = filepath.Rel(baseParent, path)
-			if err != nil {
-				return fmt.Errorf("getting relative path between %q and %q: %w", baseParent, path, err)
-			}
+		if gi.MatchesPath(relPath) || !f.MatchesPath(relPath) {
+			return nil
+		}
 
-			paths = append(paths, PathInfo{
-				Path:         path,
-				RelativePath: relPath,
-				Depth:        strings.Count(relPath, "/") + 1,
-				IsDir:        false,
-			})
+		relPath, err = filepath.Rel(baseParent, path)
+		if err != nil {
+			return fmt.Errorf("getting relative path between %q and %q: %w", basePath, path, err)
 		}
+		relPath = filepath.ToSlash(relPath)
+
+		paths = append(paths, PathInfo{
+			Path:         path,
+			RelativePath: relPath,
+			Depth:        strings.Count(relPath, "/") + 1,
+			IsDir:        false,
+		})
 		return nil
 	})
 	if err != nil {

internal/traverse_test.go

@@ -111,6 +111,14 @@ func TestTraverseDirectories(t *testing.T) {
 				"src/internal/util.go",
 			},
 		},
+		"match specific file with conflicting gitignore": {
+			directory:      filepath.Join(tmpDir, "src"),
+			filterPatterns: []string{"internal/test.txt"},
+			gitignorePaths: []string{
+				filepath.Join(tmpDir, ".gitignore"),
+			},
+			wantRelPaths: []string{},
+		},
 	}
 
 	for name, tt := range tests {

main.go

@@ -58,7 +58,7 @@ type RootCmd struct {
 	Output        string                `help:"Specifies the destination path for the output file. The file extension will automatically adjust based on the selected format (see '--format')." short:"o" type:"path" placeholder:"amalgo.txt"`
 	Stdout        bool                  `help:"Redirects all output to standard output (terminal) instead of writing to a file. Useful for piping output to other commands."`
 	Filter        []string              `help:"Controls which files are processed using glob patterns. Include patterns are processed first, then exclude patterns (prefixed with '!'). Hidden files and directories are excluded by default." short:"f" default:"*,!.*"`
-	GitIgnore     []string              `help:"Specifies .gitignore files to use for filtering. These patterns are merged with the filter patterns, taking the same precedence." name:"gitignore" short:"g"`
+	GitIgnore     []string              `help:"Specifies .gitignore files to use for filtering. These patterns are processed before the filter patterns, taking precedence. Of the provided gitignore files, the last one will take the highest precedence." name:"gitignore" short:"g"`
 	NoTree        bool                  `help:"Skips the inclusion of the file tree in the output." default:"false"`
 	NoDump        bool                  `help:"Skips the inclusion of file contents in the output." default:"false"`
 	Outline       bool                  `help:"Includes in the output a language-aware outline of code files, showing functions, classes, and other significant elements. Only available for specific file extensions: '.go'." default:"false"`

pkg/filter/filter.go

@@ -23,7 +23,17 @@ type Pattern struct {
 	Line    string
 }
 
-func (f *Filter) Merge(other *Filter) {
+// MergeWithoutPrecedence prepends the patterns of the given filter.
+// The provided patterns will be used first, meaning they may be
+// overruled by the existing patterns (on this Filter).
+func (f *Filter) MergeWithoutPrecedence(other *Filter) {
+	f.patterns = append(other.patterns, f.patterns...)
+}
+
+// MergeWithoutPrecedence appends the patterns of the given filter.
+// The provided patterns will be used last, meaning they may
+// overrule the existing patterns (on this Filter).
+func (f *Filter) MergeWithPrecedence(other *Filter) {
 	f.patterns = append(f.patterns, other.patterns...)
 }