How to merge two similar project files together?

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I've installed Ubuntu a month ago and have moved successfully from Windows. I installed the another operating system in dual-boot mode to switch between Windows & Ubuntu on startup everyday. Anyway, I installed VSC on ubuntu and pulled my project from my own git server into Xampp's htdocs folder. I didn't use git clone <url> for this. I was wondering if I could copy and paste all of the changes I've made before, but there is a big problem. After pasting the whole project to the pulled one, all of the non-changed files are recognizing as modified files by git and suddenly VSC found more than 10k changes on the repo which are waiting to be staged, committed and pushed to the server!

I tried all the solutions on the internet.

I was working on the project and saved changes, but I didn't commit and push the whole changes to the git repository. I also add some files to the projects and they need to be pushed to the repository.

By pasting the project and replacing it to the project from my windows hard drive to the htdocs located in Ubuntu os, all of the files even those which are not changed have been diagnosed as modified files by git. I don't know what is difference between two files when they're not really changed. I checked everything and connected via master branch.

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