If your project has limited free space, this can cause you not to be able to Restart the Box and also to be unable to save new content in files.
Run df -h to see how much free space you have left and if necessary review your projects contents to free up more space.
If that is heavily used (ie anything >75% as a rule) then run
sudo du -hs /var/*
this will show you more details on logs files that you can then look to clean up and free up space, especially useful if your Box is using MySQL where log files can get quite large
For more information on the df (and du) command, see http://askubuntu.com/questions/280342/why-do-df-and-du-commands-show-different-disk-usage#390301
and for tips to free up disk space, see
http://askubuntu.com/questions/5980/how-do-i-free-up-disk-space#6002