How to manage messy not staged file after migration?

Question

I just migrate from windows to linux, then Here is my git status

On branch master
Changes not staged for commit:
  (use "git add/rm <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)
  (commit or discard the untracked or modified content in submodules)

    modified:   .bowerrc
    modified:   .gitignore
    modified:   .htaccess
    modified:   .tfignore
    modified:   BuildProcessTemplates/DefaultTemplate.11.1.xaml
    modified:   BuildProcessTemplates/LabDefaultTemplate.11.xaml
    modified:   BuildProcessTemplates/UpgradeTemplate.xaml
    modified:   LICENSE.md
    modified:   README.md
    modified:   backend/assets/AppAsset.php
    modified:   backend/common/models/TbProdukEkspedisiByVendor.php
    modified:   backend/common/models/VwSalesOrderDetail.php
    modified:   backend/config/.gitignore
    modified:   backend/config/.htaccess
so on...
many files including controller, views is here

How I can move it to untracked? or How I can get clean view of git status?

Thanks in advance.