Project Site Security

I wonder if anybody is using any kind of security to SC project. I’m talking about anti-hacking tools.
Recently my SC project hosted on HostHator server got hacked. The projects used MySQL database. I haven’t checked yet what files got affected etc although this project was in Alfa testing phase so no security app was even implemented. If there was no username/password procedure I wonder how possibly this project could get hacked ?
Is it possible that Google could report this project as hacked website while it is fully legitimate ?

I would like to know what tools we have available to guard SC projects ?

Is there any effective tool to compare two sets of files (i.e original and possibly hacked set) ?
I tried some on-line services in the past but it did not work well.

Art

Since scriptcase deployments are php you can zend encode it (if your provider supports it).
Comparing two sets of files goes easily with total commander. Just point to one directory on the left and on on the right and use the Command -> Synchronise Dirs there you can do a full subdir comparison and get a very detailed view on file/line level what is different.
See www.ghisler.com for this program and totalcmd.net for many addons…

rr - Thank for replying, but my main concern is not to protect the project code from viewing but protecting the project from hackers. Of course encoding source might help but the main issue is how the hacker can get into SC project/App folder and replace some files. This relates to my other question: Where and how database access credentials are stored ?

Arthur