Can't stage after resolving conflicts during a rebase

[dbatten5]

Description

If a rebase results in a conflict, I fix the conflict and then try and stage the fixed file using s, I see a warning message that says "Conflicts must be resolved before staging" and I'm not able to stage it. However the file does stage if I do <c-s>. I'm sure this used to work fine. Interestingly when I had the diffview integration on, pressing s opened up a diffview tab, and then when I closed the tab I saw that the file was staged. Since turning off the integration I'm now seeing the warning message above.

Also, when I am able to eventually stage and commit, when I press r I used to have a popup that had continue as an option. Now when I press r I just get the main rebase menu pop up, no option to continue. It seems like neogit doesn't know that there's a rebase in progress.

Neovim version

NVIM v0.10.0
Build type: Release
LuaJIT 2.1.1716656478

Operating system and version

macOS 14.6.1

Steps to reproduce

1. Add some commits
2. Rebase with another branch that causes a conflict
3. Fix the conflict in the editor
4. Try and stage the file in the neogit console using s, see that it doesn't stage

Expected behavior

The file stages

Actual behavior

The file is not able to be staged.

Minimal config

-- NOTE: See the end of this file if you are reporting an issue, etc. Ignore all the "scary" functions up top, those are
-- used for setup and other operations.
local M = {}

local base_root_path = vim.fn.fnamemodify(debug.getinfo(1, "S").source:sub(2), ":p:h") .. "/.min"
function M.root(path)
  return base_root_path .. "/" .. (path or "")
end

function M.load_plugin(plugin_name, plugin_url)
  local package_root = M.root("plugins/")
  local install_destination = package_root .. plugin_name
  vim.opt.runtimepath:append(install_destination)

  if not vim.loop.fs_stat(package_root) then
    vim.fn.mkdir(package_root, "p")
  end

  if not vim.loop.fs_stat(install_destination) then
    print(string.format("> Downloading plugin '%s' to '%s'", plugin_name, install_destination))
    vim.fn.system({
      "git",
      "clone",
      "--depth=1",
      plugin_url,
      install_destination,
    })
    if vim.v.shell_error > 0 then
      error(string.format("> Failed to clone plugin: '%s' in '%s'!", plugin_name, install_destination),
        vim.log.levels.ERROR)
    end
  end
end

---@alias PluginName string The plugin name, will be used as part of the git clone destination
---@alias PluginUrl string The git url at which a plugin is located, can be a path. See https://git-scm.com/book/en/v2/Git-on-the-Server-The-Protocols for details
---@alias MinPlugins table<PluginName, PluginUrl>

---Do the initial setup. Downloads plugins, ensures the minimal init does not pollute the filesystem by keeping
---everything self contained to the CWD of the minimal init file. Run prior to running tests, reproducing issues, etc.
---@param plugins? table<PluginName, PluginUrl>
function M.setup(plugins)
  vim.opt.packpath = {}                      -- Empty the package path so we use only the plugins specified
  vim.opt.runtimepath:append(M.root(".min")) -- Ensure the runtime detects the root min dir

  -- Install required plugins
  if plugins ~= nil then
    for plugin_name, plugin_url in pairs(plugins) do
      M.load_plugin(plugin_name, plugin_url)
    end
  end

  vim.env.XDG_CONFIG_HOME = M.root("xdg/config")
  vim.env.XDG_DATA_HOME = M.root("xdg/data")
  vim.env.XDG_STATE_HOME = M.root("xdg/state")
  vim.env.XDG_CACHE_HOME = M.root("xdg/cache")

  -- NOTE: Cleanup the xdg cache on exit so new runs of the minimal init doesn't share any previous state, e.g. shada
  vim.api.nvim_create_autocmd("VimLeave", {
    callback = function()
      vim.fn.system({
        "rm",
        "-r",
        "-f",
        M.root("xdg")
      })
    end
  })
end

-- NOTE: If you have additional plugins you need to install to reproduce your issue, include them in the plugins
-- table within the setup call below.
M.setup({
  plenary = "https://github.com/nvim-lua/plenary.nvim.git",
  telescope = "https://github.com/nvim-telescope/telescope.nvim",
  diffview = "https://github.com/sindrets/diffview.nvim",
  neogit = "https://github.com/NeogitOrg/neogit"
})
-- WARN: Do all plugin setup, test runs, reproductions, etc. AFTER calling setup with a list of plugins!
-- Basically, do all that stuff AFTER this line.
require("neogit").setup({}) -- For instance, setup Neogit

[CKolkey]

If you manually reload neogit () after fixing the conflict in the editor, does the problem persist?

[azenan]

Have same issue w.r.t. s to stage conflict opening diffview while in merge conflict resolution. Started happening after update including the following commits:

    ● neogit 45.32ms  <leader>gg
        a1fc4e5 Merge pull request #1623 from NeogitOrg/change-process-spinner-default (2 days ago)
        8c43166 Change: config.process_spinner is now `false` by default. Too many issues with blinking cursors for users. (2 days ago)
        9ea60f7 Merge pull request #1613 from NeogitOrg/bump-ruby (2 weeks ago)
        028e9ee Bump ruby version (2 weeks ago)
        5ec2bf3 remove redundant hunks/patch - it's the same as above (2 weeks ago)
        ea99ae0 If checking out a branch fails, inform the user (2 weeks ago)
        dc411e4 Merge pull request #1611 from NeogitOrg/revert-1599-revert-hunk (2 weeks ago)
        9489f84 Revert "Add ability to revert hunk" (2 weeks ago)

Prior to this I had no issues.

[dbatten5]

If you manually reload neogit () after fixing the conflict in the editor, does the problem persist?

Yes the problem seems to persist even after reloading

[viocost]

Same issue here