Cline changes my file tree structure with the MCP server integration such that Project IDX doesn't recognize the old one

See title. My original file structure is /home/user/scaffolder-gpt-coder/ but Project IDX opens to “/home/user/Documents/Cline/MCP/web-integration-server/.idx” and treats it like that’s the default hiearchy when loading the file to the point that not even my previous version control (git) is recognized or instatiated. Is there a way to revert this change so that I do not lose any data. I would say that this happened about 5 days ago.

additional context

Project IDX opens here by default:
scaffolder-gpt-coder-1164549:~/Documents/Cline/MCP/web-integration-server$ cd /home/user/scaffolder-gpt-coder

I want it to open here and show the file structure here by default (which was the normal behavior prior to cline adding these MCP servers)
scaffolder-gpt-coder-1164549:~/scaffolder-gpt-coder{main}$ dir

claude gave me this command (terminal) which seemed to work

code /home/user/scaffolder-gpt-coder