Most complex projects have lots of files they depend on to work properly: startup and shutdown scripts, CRON jobs, log files, jar files, war files, tomcat instances, backups, third party applications, config files and SQL files to name a few.
The tendency is to deploy these files to random folders all over the server, making maintenance difficult. Where possible, put all files beneath one folder on the server.
For example, if a server is dedicated to a project called “myapp”, you could deploy everything to /myapp/*. (note how upper case letters are not used).
Exception: some companies have standard locations for installing 3rd party applications like Tomcat, so it can be appropriate to bend the rules in these cases. Symbolic links can be utilized to make files appear where they normally would.
There is also an argument for installing common programs in the default install locations, for example where you would normally find applications installed on RedHat Linux.