This week's book giveaway is in the OO, Patterns, UML and Refactoring forum. We're giving away four copies of Refactoring for Software Design Smells: Managing Technical Debt and have Girish Suryanarayana, Ganesh Samarthyam & Tushar Sharma on-line! See this thread for details.
I follow the mechanism used by Maven, even when doing builds in Ant. Basically, I do this:
1) Compile the java source files
2) Copy all of the files that make up the WAR into a directory (this is an exploded WAR)
3) Convert the directory in step 2 into a WAR file
4) Copy either the exploded WAR from step 2 or the WAR file from step 4 to Tomcat
I recommend you study Maven to see how it does this, and even if you decide not to go with Maven, follow its basic build steps (and follow its directory structure).