Thank you for the bug report

• I am using the latest version of lsp-mode related packages.
• I checked FAQ and Troubleshooting sections
• You may also try reproduce the issue using clean environment using the following command: M-x lsp-start-plain

Bug description

Commit 782e1dc by @LaurenceWarne introduced a regression and broke mypy completely for me. That happened, because I had set the same lsp-server settings that the commit modified.

Further research shown that there's nothing wrong with the commit per se, instead the problem is in how lsp-mode handles lsp-server settings. Whatever user sets with lsp-register-custom-settings is being overwritten by lsp-mode, leading to random problems like this one.

Instead lsp-register-custom-settings should not overwrite settings that a user has set.

Steps to reproduce

1. Create /tmp/.emacs with the following content:

   (package-initialize)
   (use-package lsp-mode
     :config
     (setq lsp-log-io t)
     (lsp-register-custom-settings '(("pylsp.plugins.pylsp_mypy.enabled" t t))))

2. Start emacs as emacs -Q -l /tmp/.emacs test.py
3. Start lsp-mode in the test.py buffer by evaluating M-x lsp
4. Switch to buffer with communication log by evaluating M-x lsp-workspace-show-log
5. Search for word pylsp_mypy and look at the value of enabled just below the pylsp_mypy line

Expected behavior

It is true.

Which Language Server did you use?

pylsp

OS

Linux

Error callstack

No response

Anything else?

No response