One of our recommendations is to clean up your project folder, getting rid of unnecessary content like installer cache.. One problem by doing that to early in the packaging phase is that you might need to perform self-repair on the package (ending up in the Sandbox and sbmerge it to the project folder). So one option can be to use build exclusion list. There is a documented parameter (package.ini reference guide can be found here) that will tell the build process to skip certain files, while still remaining in your project folder, making your package smaller.
The parameter is called ExcludePattern and must be placed in package.ini under its own section.
To learn more and to read the entire article at its source, please refer to the following page, VMware ThinApp Blog: Optimize the package size without deleting project content..- VMware Blogs