`git difftool` clobbers working tree, wreaking havoc

[jamilbk]

Hi there!

First, thanks for the wonderful library.

So I've been dealing with an interesting issue, and it took me a while to track it down to Mason.

I'm using Neovim v0.11.0 with the Mason plugin to install elixir_ls. This is all fine and good.

...until I run a git difftool, at which point all hell breaks loose. For context, I'm using Neovim as my difftool:

[diff]
  tool = nvimdiff
[merge]
  tool = nvimdiff
[difftool "nvimdiff"]
  cmd = nvim -f -d \"$LOCAL\" \"$REMOTE\"
[difftool]
  prompt = false

It seems that the temporary file opened in the left pane of the split is causing Mason to try and reinstall elixir-ls. When I exit the diff, git status then shows nearly all of my other working tree files to be deleted.

Here is the problematic line Mason adds to my project's .git/config after running a git difftool:

worktree = /Users/jamil/Library/Caches/mix/installs/elixir-1.18.1-erts-15.2/ddb73e4bb2c1e299782eef0365f019f3/deps/elixir_ls

I think one solution could be to disable elixir-ls LSP in diff mode, but I wanted to be sure that this isn't already supposed to be the case.

[jamilbk]

More context:

[ERROR][2025-04-28 06:51:21] ...p/_transport.lua:36     "rpc"   "elixir-ls"     "stderr"        "Running /Users/jamil/.local/share/nvim/mason/packages/elixir-ls/launch.sh\n"
[ERROR][2025-04-28 06:51:21] ...p/_transport.lua:36     "rpc"   "elixir-ls"     "stderr"        "Preferred shell is zsh, relaunching\nLooking for asdf install\n"
[ERROR][2025-04-28 06:51:21] ...p/_transport.lua:36     "rpc"   "elixir-ls"     "stderr"        "asdf executable found at /opt/homebrew/bin/asdf. Using ASDF_DIR=, ASDF_DATA_DIR=.\n"
[ERROR][2025-04-28 06:51:21] ...p/_transport.lua:36     "rpc"   "elixir-ls"     "stderr"        "Installing ElixirLS release v0.27.2\n"
[ERROR][2025-04-28 06:51:21] ...p/_transport.lua:36     "rpc"   "elixir-ls"     "stderr"        "Running in /private/var/folders/02/4nz6gzkx5wj81dkc4pf9jyyh0000gn/T/git-blob-yYPPjQ\n"
[ERROR][2025-04-28 06:51:21] ...p/_transport.lua:36     "rpc"   "elixir-ls"     "stderr"        "* Getting elixir_ls (https://github.com/elixir-lsp/elixir-ls.git - v0.27.2)\n"
[ERROR][2025-04-28 06:51:21] ...p/_transport.lua:36     "rpc"   "elixir-ls"     "stderr"        "Mix.install failed with ** (Mix.Error) Command \"git --git-dir=.git remote add origin https://github.com/elixir-lsp/elixir-ls.git\" failed with reason: fatal: not a git repository: '.git'\n\n    (mix 1.18.1) lib/mix.ex:613: Mix.raise/2\n    (mix 1.18.1) lib/mix/scm/git.ex:110: anonymous fn/2 in Mix.SCM.Git.checkout/1\n    (elixir 1.18.1) lib/file.ex:1665: File.cd!/2\n    (mix 1.18.1) lib/mix/dep/fetcher.ex:68: Mix.Dep.Fetcher.do_fetch/3\n    (mix 1.18.1) lib/mix/dep/converger.ex:238: Mix.Dep.Converger.all/9\n    (mix 1.18.1) lib/mix/dep/converger.ex:170: Mix.Dep.Converger.init_all/8\n    (mix 1.18.1) lib/mix/dep/converger.ex:110: Mix.Dep.Converger.all/4\n    (mix 1.18.1) lib/mix/dep/converger.ex:89: Mix.Dep.Converger.converge/4\n\nRetrying Mix.install with force: true\n"
[ERROR][2025-04-28 06:51:21] ...p/_transport.lua:36     "rpc"   "elixir-ls"     "stderr"        "Installing ElixirLS release v0.27.2\n"
[ERROR][2025-04-28 06:51:21] ...p/_transport.lua:36     "rpc"   "elixir-ls"     "stderr"        "Running in /private/var/folders/02/4nz6gzkx5wj81dkc4pf9jyyh0000gn/T/git-blob-yYPPjQ\n"
[ERROR][2025-04-28 06:51:21] ...p/_transport.lua:36     "rpc"   "elixir-ls"     "stderr"        "* Getting elixir_ls (https://github.com/elixir-lsp/elixir-ls.git - v0.27.2)\n"
[ERROR][2025-04-28 06:51:21] ...p/_transport.lua:36     "rpc"   "elixir-ls"     "stderr"        "** (Mix.Error) Command \"git --git-dir=.git remote add origin https://github.com/elixir-lsp/elixir-ls.git\" failed with reason: fatal: not a git repository: '.git'\n\n    (mix 1.18.1) lib/mix.ex:613: Mix.raise/2\n    (mix 1.18.1) lib/mix/scm/git.ex:110: anonymous fn/2 in Mix.SCM.Git.checkout/1\n    (elixir 1.18.1) lib/file.ex:1665: File.cd!/2\n    (mix 1.18.1) lib/mix/dep/fetcher.ex:68: Mix.Dep.Fetcher.do_fetch/3\n    (mix 1.18.1) lib/mix/dep/converger.ex:238: Mix.Dep.Converger.all/9\n    (mix 1.18.1) lib/mix/dep/converger.ex:170: Mix.Dep.Converger.init_all/8\n    (mix 1.18.1) lib/mix/dep/converger.ex:110: Mix.Dep.Converger.all/4\n    (mix 1.18.1) lib/mix/dep/converger.ex:89: Mix.Dep.Converger.converge/4\n"