You could use vim in ex and command mode, from the terminal.

To indent a single file:

vim -c "normal gg=G" -e <file-to-indent> <<'EOF'

:wq

EOF

To indent files recursively, create the following script:

indent-with-vim.sh

vim -c "normal gg=G" -e $1 <<'EOF'

:wq

EOF

Now, type:

$ chmod u+x indent-with-vim.sh

$ find . | xargs -I {} ./indent-with-vim.sh {}

Vim will do its best to reindent the files. You may improve some specific file types.

For XML:

• Install xmllint
  Add to your .vimrc

  
  
  

  au FileType xml setlocal equalprg=xmllint --format --recover - 2>/dev/null
  
  

To improve PHP formatting:

Download http://www.vim.org/scripts/download_script.php?src_id=15001
(it will download a file named php.vim)

Create the following directories on your home:

~/.vim/indent

And copy php.vim to ~/.vim/indent

If you are not satisfied with the result for any file type, you may look for alternatives on the web (like htb for HTML, https://github.com/vim-ruby/vim-ruby for improvements for Ruby, and so on).

Either way, you'd use or the .vimrc technique or the foo.vim indent file to improve the indentation.

Also, you can change the find parameters to apply to some specific types only, such as:

find . -iname "*.html" -or -iname "*.xml"