chore: add type annotations and resolve LSP warnings (#2555)

* chore: add type annotations to (almost) all functions

* stylua

* Add classes for symlink nodes

* Replace deprecated `@vararg`

* Move node classes to `node` module

* Fix `Symlink*` classes

* add vim and libuv runtime for luals, qualify libuv types

* add scripts/luals-check, not quite ready for CI

* additional nil checks for git/init.lua and git/runner.lua

* additional nil checks for nvim-tree.lua

* wrap vim.cmd-as-a-function calls inside functions

* vim.tbl_filter predicate returns booleans

* Revert "add scripts/luals-check, not quite ready for CI"

This reverts commit c70229cad9.

* Add `MinimalNode` class in `marks` module

* Fix various LSP warnings

* stylua

* Fix `Explorer` class, update related annotations and add necessary checks

* Add missing annotations to `live-filter`

* Add temporary aliases for `uv.*` types

* Resolve remaining LSP warnings

* Revert changes not related to internal types

* Minor adjustments

* Update doc comments style

* Minor adjustments (pt. 2)

---------

Co-authored-by: Alexander Courtis <alex@courtis.org>

lua/nvim-tree/git/runner.lua

@@ -2,13 +2,26 @@ local log = require "nvim-tree.log"
 local utils = require "nvim-tree.utils"
 local notify = require "nvim-tree.notify"
 
+-- TODO add "${3rd}/luv/library" to "workspace.library"
+---@class uv.uv_handle_t: table
+---@class uv.uv_stream_t: uv.uv_handle_t
+---@class uv.uv_pipe_t: uv.uv_stream_t
+
+---@class Runner
 local Runner = {}
 Runner.__index = Runner
 
 local timeouts = 0
 local MAX_TIMEOUTS = 5
 
+---@private
+---@param status string
+---@param path string|nil
 function Runner:_parse_status_output(status, path)
+  if not path then
+    return
+  end
+
   -- replacing slashes if on windows
   if vim.fn.has "win32" == 1 then
     path = path:gsub("/", "\\")
@@ -18,6 +31,10 @@ function Runner:_parse_status_output(status, path)
   end
 end
 
+---@private
+---@param prev_output string
+---@param incoming string
+---@return string
 function Runner:_handle_incoming_data(prev_output, incoming)
   if incoming and utils.str_find(incoming, "\n") then
     local prev = prev_output .. incoming
@@ -46,12 +63,15 @@ function Runner:_handle_incoming_data(prev_output, incoming)
   end
 
   for line in prev_output:gmatch "[^\n]*\n" do
-    self._parse_status_output(line)
+    self:_parse_status_output(line)
   end
 
   return ""
 end
 
+---@param stdout_handle uv.uv_pipe_t
+---@param stderr_handle uv.uv_pipe_t
+---@return table
 function Runner:_getopts(stdout_handle, stderr_handle)
   local untracked = self.list_untracked and "-u" or nil
   local ignored = (self.list_untracked and self.list_ignored) and "--ignored=matching" or "--ignored=no"
@@ -62,6 +82,7 @@ function Runner:_getopts(stdout_handle, stderr_handle)
   }
 end
 
+---@param output string
 function Runner:_log_raw_output(output)
   if log.enabled "git" and output and type(output) == "string" then
     log.raw("git", "%s", output)
@@ -69,12 +90,17 @@ function Runner:_log_raw_output(output)
   end
 end
 
+---@param callback function|nil
 function Runner:_run_git_job(callback)
   local handle, pid
   local stdout = vim.loop.new_pipe(false)
   local stderr = vim.loop.new_pipe(false)
   local timer = vim.loop.new_timer()
 
+  if stdout == nil or stderr == nil or timer == nil then
+    return
+  end
+
   local function on_finish(rc)
     self.rc = rc or 0
     if timer:is_closing() or stdout:is_closing() or stderr:is_closing() or (handle and handle:is_closing()) then
@@ -151,6 +177,7 @@ function Runner:_wait()
   end
 end
 
+---@param opts table
 function Runner:_finalise(opts)
   if self.rc == -1 then
     log.line("git", "job timed out  %s %s", opts.toplevel, opts.path)
@@ -167,9 +194,9 @@ function Runner:_finalise(opts)
 end
 
 --- Runs a git process, which will be killed if it takes more than timeout which defaults to 400ms
---- @param opts table
---- @param callback function|nil executed passing return when complete
---- @return table|nil status by absolute path, nil if callback present
+---@param opts table
+---@param callback function|nil executed passing return when complete
+---@return table|nil status by absolute path, nil if callback present
 function Runner.run(opts, callback)
   local self = setmetatable({
     toplevel = opts.toplevel,