bug: Chekout failed. Cannot update submodule: .github/nvim_doc_tools

[aravezskinteeth]

Neovim version (nvim -v)

0.9.9

Operating system/version

MacOS 12.6.2

Output of :AerialInfo

E492: Not an editor command: AerialInfo

Describe the bug

I have AstroNvim and use Lazy to manage my plugin updates, but for some reason I cannot manage to update it because I get the following errors:

checkout failed
error: Entry '.github/nvim_doc_tools/apidoc.py' not uptodate. Cannot merge.
error: Submodule '.github/nvim_doc_tools' could not be updated.
error: Cannot update submodule: .github/nvim_doc_tools

Aborting

Steps To Reproduce

In the terminal with AstroNvim and Lazy

1. nvim
2. :Lazy
3. It tells me aerial.nvim needs to be updated so I press U
4. I get the error message on the screnshot.

Expected Behavior

To get aerial.nvim to update.

Minimal example file

No response

Minimal init.lua

return {
  -- Configure AstroNvim updates
  updater = {
    remote = "origin",     -- remote to use
    channel = "stable",    -- "stable" or "nightly"
    version = "latest",    -- "latest", tag name, or regex search like "v1.*" to only do updates before v2 (STABLE ONLY)
    branch = "nightly",    -- branch name (NIGHTLY ONLY)
    commit = nil,          -- commit hash (NIGHTLY ONLY)
    pin_plugins = nil,     -- nil, true, false (nil will pin plugins on stable only)
    skip_prompts = false,  -- skip prompts about breaking changes
    show_changelog = true, -- show the changelog after performing an update
    auto_quit = false,     -- automatically quit the current session after a successful update
    remotes = {            -- easily add new remotes to track
      --   ["remote_name"] = "https://remote_url.come/repo.git", -- full remote url
      --   ["remote2"] = "github_user/repo", -- GitHub user/repo shortcut,
      --   ["remote3"] = "github_user", -- GitHub user assume AstroNvim fork
    },
  },
   -- Set colorscheme to use
  colorscheme = "catppuccin-macchiato",
 -- Diagnostics configuration (for vim.diagnostics.config({...})) when diagnostics are on
  diagnostics = {
    virtual_text = true,
    underline = true,
  },
  lsp = {
    -- customize lsp formatting options
    formatting = {
      -- control auto formatting on save
      format_on_save = {
        enabled = false,    -- enable or disable format on save globally
        allow_filetypes = { -- enable format on save for specified filetypes only
          -- "go",
        },
        ignore_filetypes = { -- disable format on save for specified filetypes
          -- "python",
        },
      },
      disabled = { -- disable formatting capabilities for the listed language servers
        -- disable lua_ls formatting capability if you want to use StyLua to format your lua code
        -- "lua_ls",
      },
      timeout_ms = 1000, -- default format timeout
      -- filter = function(client) -- fully override the default formatting function
      --   return true
      -- end
    },
    -- enable servers that you already have installed without mason
    servers = {
      -- pyright,
    }
  },
  -- Configure require("lazy").setup() options
  lazy = {
    defaults = { lazy = true },
    performance = {
      rtp = {
        -- customize default disabled vim plugins
        disabled_plugins = { "tohtml", "gzip", "matchit", "zipPlugin", "netrwPlugin", "tarPlugin" },
      },
    },
  },
  end,
}

Additional context

Full astronvim user config is here

[stevearc]

Not sure why there would be problems, as the submodule ref has been pushed and I haven't done anything funky with the git history. Try uninstalling and reinstalling (in Lazy parlance, a "clean" which you can do with x)

[aravezskinteeth]

You're right I have no idea why I got this weird error. It's already solved by reinstalling again. Thank you.