Preferred scripting capabilities on iPhone?

How would you achieve moving all files except certain named ones into a certain folder, on iPhone?

Would you use a specific plugin, or is there a most generalizable way to automate things in general, like that?

A-Shell app or iSH. You can even learn of them on this forum (git syncing related threads).
Best experience (for me) is through jailbreak and local SSH through Shortcuts. One can run Python scripts, etc.
There’s also Scriptable with js in Shortcuts. In A-Shell, you can pwd your Obsidian vault’s path complete with UUID (which path, alas, changes on each app update).

Obsidian plugins? Templater can be used with js, but there’ll be probably limitations accessing the file system. For more of these kinds of info, you’ll need to look around in the Developer section.

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Let me add that it’s generally better to keep a laptop or desktop and perform potentially destructive operations there. With GitHub Desktop (and git) installed, you can see what you have been up to and revert to an earlier state if you have mucked things up.

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Thanks. So to make sure I fully grasp this:

There is something about the file system on iOS where someone could not just write an Obsidian plugin which is able to automatically modify the location of the app’s files? Or has no one made such a plug in yet?

App’s files – a rather vague thing.
I take it you want file operations on notes while on iOS? Then take a look at the File Cooker plugin that can be used for moving files to a folder based on search results.
You don’t need scripting with that.

Kudos to the person bringing up this plugin the other day.