Currently, the setup() function in config.lua reassigns the entire module table M to a new table returned by vim.tbl_extend. As a result, any existing references to the original M (such as the one returned when requiring the module) becomes stale. This causes inconsistent behavior where:

• accessing keys from the table returned by require("java-deps.config") will result in the old values (ignoring any user supplied config).
• functions within the module (like config.get_split_command() or config.has_numbers()) uses the new values (the ones from the user config).

That is because they are operating on different tables.

a minimal example that showcases the issue:

local function require_config()
    local M = {
        key = "original value"
    }
    M.setup = function (config)
        if config then
            M = vim.tbl_extend("force", M, config)
        end
    end
    M.get_key = function ()
        return M.key
    end
    return M
end

local config = require_config()
config.setup({ key = "new value"})
print(config.key)
print(config.get_key())

This will output

original value
new value

To fix this, I merged the new configuration directly into the existing M table. I also changed vim.tbl_extend to vim.tbl_deep_extend since the config has nested tables. There are other ways to fix this, but I think this approach minimize changes to the current codebase.