It may be better to initialize ContextMenu to nil and move all the initialization and menu items registration into a coroutine using core.add_thread() that performs the config.plugins.contextmenu availability check. This way you properly ensure the plugin is really disabled after everything is loaded up preventing possible issues.

@jgmdev is this what you meant? If so, I guess I'll do the same in lite-xl/lite-xl-plugins#267

It seems to be working.
However if [settings] plugin is enabled and [contextmenu] is turned on, turning it off via project module is useless as [settings] loads [contextmenu] anyway.

In our case this is tolerable, we can live without [settings] and manage config, style etc. in project module.
Managing project module is a lot easier than having to maintain a separate portable build only for a single project.

@jgmdev is this what you meant? If so, I guess I'll do the same in lite-xl/lite-xl-plugins#267

exactly

It seems to be working. However if [settings] plugin is enabled and [contextmenu] is turned on, turning it off via project module is useless as [settings] loads [contextmenu] anyway.

Maybe this change could fix the issue, haven't tested it:

diff --git a/data/plugins/settings.lua b/data/plugins/settings.lua
index cc29090f..c0c4dcd5 100644
--- a/data/plugins/settings.lua
+++ b/data/plugins/settings.lua
@@ -1543,6 +1543,9 @@ function Settings:load_plugin_settings()
           settings.config.enabled_plugins
           and
           settings.config.enabled_plugins[plugin]
+          and
+          --ensure plugin is not disabled on user or project module
+          config.plugins[plugin] ~= false
         )
       then
         enabled = true
@@ -1877,7 +1880,7 @@ function core.run()
   -- load plugins disabled by default and enabled by user
   if settings.config.enabled_plugins then
     for name, _ in pairs(settings.config.enabled_plugins) do
-      if not config.plugins[name] then
+      if config.plugins[name] == nil then
         require("plugins." .. name)
       end
     end