@lunatikz: If this is a one-time thing for some apps you compiled, you can add the full path and name for each of the individual files inside your /opt/.filetool.lst file. Well, not quite the fully qualified path... omit the initial /, like you will see for the other files listed there. Then your normal backup/restore will include these files. This is needed for anything you want to save and restore under /usr, /etc, /bin, /sbin, etc.
There are also scripts that can help you make a custom .tcz extension file. The TinyCore wiki has some notes on that. In the Programming Sub-forum, there are example custom applications that have such scripts. Give me a minute and I'll attach a sample from one of my projects... OK, done. If you make any of these apps into extensions, maybe you would submit them to the repository? At least if you think there are any other users for them.
Note that this script includes some assumptions, such as the icon file is the same as the program plus ".png". You may need to adjust the script for the apps you want.
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Mike Lockmoore