Also built my own MCP server off the back of this article. I too have noticed during refactors that Coding agents take the long way around to move things to other files, and it can cause errors in the process (and burn tokens). Here's my attempt at the solution, with an encrypted data store and undo operations. Give it a try and see if you like it: https://github.com/Pr0j3c7t0dd-Ltd/cut-copy-paste-mcp