Moved from this topic.
I’m having the same exact problem right now. I can either remove “/kirby” in the url OR get the panel to work, but not both. I really want to install Kirby to a subfolder for organization reasons.
So it’s OK for you to have /kirby in the URL? This should generally work.
I would highly prefer to have Kirby installed in a subfolder while hiding “/kirby” in the URL. This is for a business website, not for a casual site 
Right now I have Kirby installed to the root to have the panel working. I am hoping this issue will be solved at a later time and I will be able to transfer my files to a subfolder. Would be awesome also for the future solution to be documented.
So why do you need to install Kirby in a subdirectory? I don’t really get why you would want to have something in a subdirectory and then fake the root level to be honest. This makes the root level unusable for other stuff anyway.
I agree with @lukasbestle. Putting Kirby into a subfolder would only make sense if you have several domains in separate folders on the same server, but then you should be able to point the customer domain to the subfolder in the domain settings. But then you would not need the additional .htaccess rules and all would be fine.
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