diff --git a/utils/modifycommand_path_resolution_test.go b/utils/modifycommand_path_resolution_test.go
new file mode 100644
index 0000000..7875f04
--- /dev/null
+++ b/utils/modifycommand_path_resolution_test.go
@@ -0,0 +1,303 @@
+package utils
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+)
+
+func TestAggregateGlobsWithSourceDir(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "aggregate-globs-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create a subdirectory structure
+	subDir := filepath.Join(tmpDir, "subdir")
+	err = os.MkdirAll(subDir, 0755)
+	assert.NoError(t, err)
+
+	// Create test files
+	testFile := filepath.Join(subDir, "test.xml")
+	err = os.WriteFile(testFile, []byte("<test/>"), 0644)
+	assert.NoError(t, err)
+
+	commands := []ModifyCommand{
+		{
+			Name:      "test1",
+			Files:     []string{"subdir/*.xml"},
+			SourceDir: tmpDir,
+		},
+		{
+			Name:      "test2",
+			Files:     []string{"*.txt"},
+			SourceDir: tmpDir,
+		},
+	}
+
+	globs := AggregateGlobs(commands)
+
+	// Both should be resolved relative to tmpDir
+	expectedSubdir := ResolvePath(filepath.Join(tmpDir, "subdir/*.xml"))
+	expectedTxt := ResolvePath(filepath.Join(tmpDir, "*.txt"))
+
+	assert.Contains(t, globs, expectedSubdir, "Should contain resolved subdir glob")
+	assert.Contains(t, globs, expectedTxt, "Should contain resolved txt glob")
+	assert.Len(t, globs, 2, "Should have 2 unique globs")
+}
+
+func TestAggregateGlobsWithAbsolutePaths(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "aggregate-globs-abs-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	absPath := ResolvePath(tmpDir)
+
+	commands := []ModifyCommand{
+		{
+			Name:      "test1",
+			Files:     []string{absPath + "/*.xml"},
+			SourceDir: tmpDir, // SourceDir should be ignored for absolute paths
+		},
+	}
+
+	globs := AggregateGlobs(commands)
+
+	// Absolute path should be used as-is (after ResolvePath normalization)
+	expected := ResolvePath(absPath + "/*.xml")
+	assert.Contains(t, globs, expected, "Should contain absolute path glob")
+	assert.Len(t, globs, 1, "Should have 1 glob")
+}
+
+func TestAggregateGlobsWithoutSourceDir(t *testing.T) {
+	cwd, err := os.Getwd()
+	assert.NoError(t, err)
+
+	commands := []ModifyCommand{
+		{
+			Name:      "test1",
+			Files:     []string{"*.xml"},
+			SourceDir: "", // No SourceDir
+		},
+	}
+
+	globs := AggregateGlobs(commands)
+
+	// Without SourceDir, should resolve relative to CWD
+	expected := ResolvePath(filepath.Join(cwd, "*.xml"))
+	assert.Contains(t, globs, expected, "Should resolve relative to CWD when SourceDir is empty")
+}
+
+func TestAggregateGlobsConsistentRegardlessOfCWD(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "aggregate-globs-cwd-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create test structure
+	testFile := filepath.Join(tmpDir, "test.xml")
+	err = os.WriteFile(testFile, []byte("<test/>"), 0644)
+	assert.NoError(t, err)
+
+	commands := []ModifyCommand{
+		{
+			Name:      "test",
+			Files:     []string{"test.xml"},
+			SourceDir: tmpDir,
+		},
+	}
+
+	// Get original CWD
+	originalCwd, err := os.Getwd()
+	assert.NoError(t, err)
+	defer os.Chdir(originalCwd)
+
+	// Test from original directory
+	globs1 := AggregateGlobs(commands)
+	expected1 := ResolvePath(filepath.Join(tmpDir, "test.xml"))
+
+	// Change to tmpDir
+	err = os.Chdir(tmpDir)
+	assert.NoError(t, err)
+
+	// Test from tmpDir - should produce same result
+	globs2 := AggregateGlobs(commands)
+	expected2 := ResolvePath(filepath.Join(tmpDir, "test.xml"))
+
+	// Both should resolve to the same absolute path
+	assert.Equal(t, expected1, expected2, "Paths should be identical regardless of CWD")
+	assert.Contains(t, globs1, expected1, "First run should contain expected path")
+	assert.Contains(t, globs2, expected2, "Second run should contain expected path")
+	assert.Equal(t, globs1, globs2, "Globs should be identical regardless of CWD")
+}
+
+func TestAssociateFilesWithCommandsSourceDir(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "associate-files-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create test structure
+	subDir := filepath.Join(tmpDir, "data")
+	err = os.MkdirAll(subDir, 0755)
+	assert.NoError(t, err)
+
+	testFile := filepath.Join(subDir, "test.xml")
+	err = os.WriteFile(testFile, []byte("<test/>"), 0644)
+	assert.NoError(t, err)
+
+	commands := []ModifyCommand{
+		{
+			Name:      "test",
+			Regex:     "pattern",
+			Lua:       "expr",
+			Files:     []string{"data/test.xml"},
+			SourceDir: tmpDir,
+		},
+	}
+
+	files := []string{testFile}
+	associations, err := AssociateFilesWithCommands(files, commands)
+	assert.NoError(t, err)
+
+	// File should be associated with command
+	assert.Contains(t, associations, testFile, "File should be in associations")
+	association := associations[testFile]
+	assert.Len(t, association.Commands, 1, "Should have 1 command")
+	assert.Equal(t, "test", association.Commands[0].Name, "Command name should match")
+}
+
+func TestAssociateFilesWithCommandsAbsolutePath(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "associate-files-abs-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	testFile := filepath.Join(tmpDir, "test.xml")
+	err = os.WriteFile(testFile, []byte("<test/>"), 0644)
+	assert.NoError(t, err)
+
+	absPath := ResolvePath(testFile)
+
+	commands := []ModifyCommand{
+		{
+			Name:      "test",
+			Regex:     "pattern",
+			Lua:       "expr",
+			Files:     []string{absPath},
+			SourceDir: tmpDir, // Should be ignored for absolute paths
+		},
+	}
+
+	files := []string{testFile}
+	associations, err := AssociateFilesWithCommands(files, commands)
+	assert.NoError(t, err)
+
+	// File should be associated
+	assert.Contains(t, associations, testFile, "File should be in associations")
+	association := associations[testFile]
+	assert.Len(t, association.Commands, 1, "Should have 1 command")
+}
+
+func TestAssociateFilesWithCommandsNoSourceDir(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "associate-files-no-sourcedir-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	testFile := filepath.Join(tmpDir, "test.xml")
+	err = os.WriteFile(testFile, []byte("<test/>"), 0644)
+	assert.NoError(t, err)
+
+	// Use absolute path since we have no SourceDir
+	absPath := ResolvePath(testFile)
+
+	commands := []ModifyCommand{
+		{
+			Name:      "test",
+			Regex:     "pattern",
+			Lua:       "expr",
+			Files:     []string{absPath},
+			SourceDir: "", // No SourceDir
+		},
+	}
+
+	files := []string{testFile}
+	associations, err := AssociateFilesWithCommands(files, commands)
+	assert.NoError(t, err)
+
+	// File should be associated
+	assert.Contains(t, associations, testFile, "File should be in associations")
+	association := associations[testFile]
+	assert.Len(t, association.Commands, 1, "Should have 1 command")
+}
+
+func TestSourceDirConditionCoverage(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "sourcedir-condition-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	tests := []struct {
+		name      string
+		glob      string
+		sourceDir string
+		shouldResolve bool
+	}{
+		{
+			name:      "Relative path with SourceDir",
+			glob:      "test.xml",
+			sourceDir: tmpDir,
+			shouldResolve: true,
+		},
+		{
+			name:      "Absolute path with SourceDir",
+			glob:      ResolvePath(filepath.Join(tmpDir, "test.xml")),
+			sourceDir: tmpDir,
+			shouldResolve: false, // Should use absolute path as-is
+		},
+		{
+			name:      "Relative path without SourceDir",
+			glob:      "test.xml",
+			sourceDir: "",
+			shouldResolve: false, // Should resolve relative to CWD
+		},
+		{
+			name:      "Absolute path without SourceDir",
+			glob:      ResolvePath(filepath.Join(tmpDir, "test.xml")),
+			sourceDir: "",
+			shouldResolve: false, // Should use absolute path as-is
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			commands := []ModifyCommand{
+				{
+					Name:      "test",
+					Files:     []string{tt.glob},
+					SourceDir: tt.sourceDir,
+				},
+			}
+
+			globs := AggregateGlobs(commands)
+			assert.Len(t, globs, 1, "Should have 1 glob")
+
+			var resolvedGlob string
+			for g := range globs {
+				resolvedGlob = g
+			}
+
+			if tt.shouldResolve {
+				// Should be resolved relative to SourceDir
+				expected := ResolvePath(filepath.Join(tt.sourceDir, tt.glob))
+				assert.Equal(t, expected, resolvedGlob, "Should resolve relative to SourceDir")
+			} else if filepath.IsAbs(tt.glob) {
+				// Absolute path should be normalized but not changed
+				expected := ResolvePath(tt.glob)
+				assert.Equal(t, expected, resolvedGlob, "Absolute path should be normalized")
+			} else {
+				// Relative path without SourceDir should resolve to CWD
+				cwd, _ := os.Getwd()
+				expected := ResolvePath(filepath.Join(cwd, tt.glob))
+				assert.Equal(t, expected, resolvedGlob, "Should resolve relative to CWD")
+			}
+		})
+	}
+}