A new document is untitled. You are asked for a file name when you save it the first time (using Cmd-S for example).

When you save a new file, you can choose iCloud as the destination in the "Where" dropdown.

You can also use the File -> Move To... command to move a file to iCloud.

Or you can move your mouse cursor over the file name in the window title bar, click on the triangle that appears next to the file name and choose "Move to iCloud...".

If you open the File menu and press the Alt key on your keyboard, the "Duplicate" command becomes "Save As...".

So there are many ways to save, move or copy a file to iCloud.

I found this in Apple's docs:

Note: If your app needs to create executable files that are typically executed in some way other than through Launch Services (shell scripts, for example), you should also specify the com.apple.security.files.user-selected.executable entitlement.
By default, when writing executable files in sandboxed apps, the files are quarantined. Gatekeeper prevents quarantined executable files and other similar files (shell scripts, web archives, and so on) from opening or executing unless the user explicitly launches them from Finder.
If those executables are tools that are intended to run from the command line, such as shell scripts, this presents a problem. With this flag, the file quarantine system allows the app to write non-quarantined executables so that Gatekeeper does not prevent them from executing.

Currently, Textastic does not specify this entitlement. Since it is a sandboxed app, executable files are quarantined by the Mac OS X sandbox when Textastic saves them.

I will add this entitlement in the next update.

Interesting. Can you tell me the exact steps that are needed to reproduce the issue?

Thanks you! I thought that was the problem, I just wanted to make sure :)

I just found this issue in my todo list and wanted to fix it, but the screenshots seem to be gone. Do you still have the screenshots?

This should be fixed in the next update.

The next version of Textastic will allow cut and paste even when the keyboard is not up.