If I may, I would like to repeat here what is my (simple) personal opinion about automatic-indentation applications (since we talked about that with vicente with private message, if I remember correctly).
Sometimes, you need to adjust indentation manually (*), not strictly following the indent rules, just because the code looks better like this and is more readable. Automatic tools just don't care about that.
That's not a total no-go with these tools, but I really think that it's quite easy to adapt our style to a specific project. I do it all day at work, in facts
One can also use his "indenter" only on his part of the source code just before commiting. Some text editors allows to indent only the current selection for instance.
(*) multilines "if" statements, half(-half) tabulations, long lines, ...