Cloning root site when WP is in its own folder

I think issue #2 is fairly straightforward. The Cloner can’t tell what other tables plugins might install at the global level and thus when cloning the root site could potentially create junk tables in clones. This is one of the reasons we originally didn’t allow / support ID = 1 cloning ?? We currently exclude well-known table names from other plugins like BuddyPress on root cloning, and can add those tables to the exclusion. Thank you for reporting that!!! It’s the only way we know we need to add things like that (can’t try every plugin out there ?? )

What can we help with on issue #1? I don’t think it’s going to be possible to get that to work if WP is installed in /app/ without a custom exception for that scenario. In order to automate things like the Cloner does, it’s expecting standard configurations where WP is installed at the root of a TLD. It can work in other scenarios too, but can also have unpredictable results sometimes in some situations.

As a work-around, you might be able to check your site and home URL fields and update those. Not sure if it will fix the path issue or not.
Network Dashboard > Sites > All Sites > [hover site name] Edit > Settings [tab] >
site url field
home url field

What is in those? Does that help?

Issue #1
I solved the problem modifying the siteurl field in the Options table for blog_id 4, I forgot it can be done in the settings tab as you pointed out

I think your plugin can deal with WP installations in its own folder quite easy. When cloning the main site, discard that folder in the siteurl field. As Multisite directories are virtual, not real ones, the WP folder is only used in the main site
Siteurl
https://wpmultisite.loc/app
https://wpmultisite.loc/es
https://wpmultisite.loc/fr
https://wpmultisite.loc/it

Issue #2
You face a huge problem taking into account there’re so many plugins. For me, a good solution would be presenting a list with non-standard WP tables and let the users, if they know/want, select wich ones shouldn’t be copied. But I understand the “Decisions, not Options” principle in WP philosophy. May be the WP team should recommend to plugin developers the use of an standard second prefix in additional tables

Another great plugin with additional tables:
Posts 2 Posts: p2p, p2pmeta

Thanks for your help, I’ll recommend your plugin

Thank you for your suggestions on issue #1 – we’re rewriting the plugin to v3 and have put this in our todo list of fixes.

Great point for #2… we’re working on this also just to provide more flexibility, but I hadn’t thought about it solving that particular scenario too, which it would quite nicely.

Thanks for all your feedback!