I am launching the production Project Ive been working on and noticed that the Deploy zip file includes old applications that I have deleted.
I tried exporting the project and then importing it… it looks fine in Scriptcase but when I deploy they are still there.
I noticed in the exported .ZIP file that in the “apl” folder there are .bkp files for each of my old applications that I deleted.
How can I delete an application and it be gone for real? I don’t want to publish things I don’t need.
The php files is the result of a generation process. If you delete an application it is deleted from the sqlite database, but the result is kept. In your sc instance you need to locate the generated files and the most easy way is to delete all, and then do a full regenerate. But you can delete the subdirs of the applications that where deleted manual too. I’m lazy 
Thanks Albert! That really helped a lot. Im publishing a clean project now!
Delete too tmp folder inside SC. Sometimes goes crazy and mix things (an app deployment confuses with a full deployment)