I'm surprised you managed to get Desktop running on Linux lol. You don't need the filesystem/git MCPs alongside codemcp; in fact, it's better not to have them so that Claude consistently uses' codemcp's equivalents to do edits. I'm not sure why codemcp's built-in git support did not work; you can probably find out more by looking in .codemcp/codemcp.log.

If you need to start a new chat, it works just fine. Tell Claude what's happened so far and what you want it to do. You can also ask Claude to summarize the old conversation, that's how /compact in claude code works too.