diff --git a/core/handlers/vault/initialize_handler.go b/core/handlers/vault/initialize_handler.go
index ac75b4e..7be6f3c 100644
--- a/core/handlers/vault/initialize_handler.go
+++ b/core/handlers/vault/initialize_handler.go
@@ -11,9 +11,11 @@ import (
 )
 
 type initializeCommand struct {
-	VaultName         string `json:"vaultName"`
-	VaultPath         string `json:"vaultPath"`
-	TemplateDirectory string `json:"templateDirectory"`
+	VaultName              string   `json:"vaultName"`
+	VaultPath              string   `json:"vaultPath"`
+	TemplateDirectory      string   `json:"templateDirectory"`
+	ExcludeIndexFiles      []string `json:"excludeIndexFiles"`
+	OverrideDefaultIgnores bool     `json:"overrideDefaultIgnores"`
 }
 
 type InitializeHandler struct {
@@ -32,7 +34,12 @@ func (h InitializeHandler) Handle(ctx context.Context, raw json.RawMessage) (any
 		return nil, err
 	}
 
-	store := store.NewVaultStore(cmd.VaultName, cmd.VaultPath, cmd.TemplateDirectory)
+	store := store.NewVaultStore(
+		cmd.VaultName, 
+		cmd.VaultPath, 
+		cmd.TemplateDirectory, 
+		cmd.ExcludeIndexFiles,
+		cmd.OverrideDefaultIgnores)
 
 	err := persistence.InitializeDBContext(store.Config.VaultName())
 	if err != nil {
diff --git a/core/services/index_rebuilder.go b/core/services/index_rebuilder.go
index a3939e3..e810b91 100644
--- a/core/services/index_rebuilder.go
+++ b/core/services/index_rebuilder.go
@@ -8,10 +8,11 @@ import (
 	"slices"
 	"strings"
 
-	filehandling "github.com/KristianJBorgwarth/dendrite.daemon/core/file_handling"
+	"github.com/KristianJBorgwarth/dendrite.daemon/core/file_handling"
 	"github.com/KristianJBorgwarth/dendrite.daemon/core/models"
 	"github.com/KristianJBorgwarth/dendrite.daemon/persistence"
 	"github.com/KristianJBorgwarth/dendrite.daemon/persistence/repositories"
+	"github.com/KristianJBorgwarth/dendrite.daemon/persistence/store"
 )
 
 type IIndexRebuilder interface {
@@ -136,7 +137,7 @@ func (r *indexRebuilder) readFiles(vault string) ([]*filehandling.File, error) {
 }
 
 func (r *indexRebuilder) IsValidDirectory(path string) bool {
-	ignoredDirs := []string{".git", ".templates", "temp"}
+	ignoredDirs := store.GetVaultStore().GetExcludeIndexFiles()
 	for part := range strings.SplitSeq(path, string(filepath.Separator)) {
 		if slices.Contains(ignoredDirs, part) {
 			return false
diff --git a/dendrite b/dendrite
index 73a4b73..0e49273 100755
Binary files a/dendrite and b/dendrite differ
diff --git a/persistence/config/vault_configuration.go b/persistence/config/vault_configuration.go
index 6d1df17..0d3e031 100644
--- a/persistence/config/vault_configuration.go
+++ b/persistence/config/vault_configuration.go
@@ -1,13 +1,28 @@
 package persistenceconfig
 
 type VaultConfiguration struct {
-	name              string
-	path              string
-	templateDirectory string
+	name                   string
+	path                   string
+	templateDirectory      string
+	exludeIndexFiles       []string
+	defaultExcludes        []string
+	overrideDefaultIgnores bool
 }
 
-func NewVaultConfiguration(vaultName, vaultPath, templateDirectory string) *VaultConfiguration {
-	return &VaultConfiguration{name: vaultName, path: vaultPath, templateDirectory: templateDirectory}
+func NewVaultConfiguration(
+	vaultName,
+	vaultPath,
+	templateDirectory string,
+	excludeIndexFiles []string,
+	overrideDefaultIgnores bool,
+) *VaultConfiguration {
+	return &VaultConfiguration{
+		name:              vaultName,
+		path:              vaultPath,
+		templateDirectory: templateDirectory,
+		exludeIndexFiles:  excludeIndexFiles,
+		defaultExcludes:   []string{".git", ".templates"},
+	}
 }
 
 func (vc *VaultConfiguration) VaultName() string {
@@ -21,3 +36,15 @@ func (vc *VaultConfiguration) VaultPath() string {
 func (vc *VaultConfiguration) TemplateDirectory() string {
 	return vc.templateDirectory
 }
+
+func (vc *VaultConfiguration) ExcludeIndexFiles() []string {
+	return vc.exludeIndexFiles
+}
+
+func (vc *VaultConfiguration) GetExcludeIndexFiles() []string {
+	defaultIgnores := []string{".git", ".templates"}
+	if vc.overrideDefaultIgnores {
+		return vc.exludeIndexFiles
+	}
+	return append(defaultIgnores, vc.exludeIndexFiles...)
+}
diff --git a/persistence/store/vault_store.go b/persistence/store/vault_store.go
index d557a5a..ef82e20 100644
--- a/persistence/store/vault_store.go
+++ b/persistence/store/vault_store.go
@@ -12,11 +12,23 @@ type VaultStore struct {
 
 var vaultStore *VaultStore
 
-func NewVaultStore(vaultName, vaultPath, templateDir string) *VaultStore {
+func NewVaultStore(
+	vaultName,
+	vaultPath,
+	templateDir string,
+	exludeIndexFiles []string,
+	overrideDefaultIgnores bool,
+) *VaultStore {
 	if vaultStore != nil {
 		return vaultStore
 	}
-	vaultStore = &VaultStore{Config: persistenceconfig.NewVaultConfiguration(vaultName, vaultPath, templateDir)}
+	vaultStore = &VaultStore{Config: persistenceconfig.NewVaultConfiguration(
+		vaultName,
+		vaultPath,
+		templateDir,
+		exludeIndexFiles,
+		overrideDefaultIgnores,
+	)}
 	return vaultStore
 }
 
@@ -44,3 +56,6 @@ func (vs *VaultStore) fileTypeCheck(templateName string) string {
 	return templateName
 }
 
+func (vs *VaultStore) GetExcludeIndexFiles() []string {
+	return vs.Config.GetExcludeIndexFiles()
+}
diff --git a/test/test_integration/main_test.go b/test/test_integration/main_test.go
index 77553a6..c7455bd 100644
--- a/test/test_integration/main_test.go
+++ b/test/test_integration/main_test.go
@@ -46,7 +46,7 @@ func NewDBFixture() *DBFixture {
 		DB:          dbContext.DB,
 		DBPath:      dbPath,
 		TestContext: context.Background(),
-		VaultStore:  store.NewVaultStore("testVault", vaultPath, path.Join(vaultPath, "templates")),
+		VaultStore:  store.NewVaultStore("testVault", vaultPath, path.Join(vaultPath, "templates"), []string{}, false),
 	}
 }